Create Publication-Quality Plots

Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals.


News

BoutrosLab.plotting.general 5.9.2 2018-04-10

FEATURE

  • Legend grob for continous legends now auto place themselves -- x and y pos dont do anything anymore
  • Print to file will now override previous entries
  • removed printing for individual plot info (too unreliable)

BoutrosLab.plotting.general 5.9.1 2018-04-04

FEATURE

  • Multipanel plot now uses tob axis labels too for lining up plots

BUG

  • Multipanel plot now correctly positions plot main labels

BoutrosLab.plotting.general 5.9.0 2018-03-23

FEATURE

  • added code for saving data information and trellis object information to each relevant plot

BoutrosLab.plotting.general 5.8.16 2018-03-16

FEATURE

  • cleaned up the multipanelplot code and updated the examples

BoutrosLab.plotting.general 5.8.15 2018-03-13

FEATURE

  • made multipanelplot legend/label placement algorithm more optimal

BoutrosLab.plotting.general 5.8.14 2018-03-09

FEATURE

  • now stores data on the mount

BUG

  • text now passed to panel in seperate list, stopping it from being reset in between plots

BoutrosLab.plotting.general 5.8.13 2018-02-13

FEATURE

  • adjusted polygon plot to work well with roc plot

BoutrosLab.plotting.general 5.8.12 2018-02-08

FEATURE

  • added lollipop plot as an extension of scatterplot

BoutrosLab.plotting.general 5.8.11 2018-02-05

FEATURE

  • added ability to disable factor sorting in relative plots
  • added example to histogram of type change

BoutrosLab.plotting.general 5.8.10 2018-01-22

FEATURE

  • added border colour for histogram bars

BoutrosLab.plotting.general 5.8.9 2018-01-12

FEATURE

  • added inside legend auto finder code

BUG

  • boxplot addstriplot colour was having issue with multiple boxplots, now works properly

BoutrosLab.plotting.general 5.8.8 2017-12-19

UPDATE

  • updated formatting to match coding standard
  • added inside legends to multipanel plot

BUG

  • heatmap now accepts both x and y axis covariates

BoutrosLab.plotting.general 5.8.7 2017-11-15

UPDATE

  • updated formatting to match coding standard

BoutrosLab.plotting.general 5.8.6 2017-11-15

FEATURE

  • legend and covariate grobs can now use x and y coordinates

BUG

  • heatmap using colours must faster
  • legacy settings in multipanel plot now affect all individual plots too

BoutrosLab.plotting.general 5.8.5 2017-11-01

FEATURE

  • force colour scheme now has heteroplasmy fraction and MT annotation

BoutrosLab.plotting.general 5.8.4 2017-10-25

BUG FIX

  • Multipanel plot now accepts colorkey and draw key legends
  • Get defaults now retrieves ArialMT instead of Arial font (actual name on Linux)

FEATURE

  • heatmap can now use colours to specify the squares
  • density plot can now add text (like bar/boxplot)

BoutrosLab.plotting.general 5.8.3 2017-08-11

BUG FIX

  • Multipanel plot now works with legends from original plots
  • Barplot error bars now work with horizontal plots too

FEATURE

  • heatmap now accepts inside legends and can specify text not based on grid cooridnates

BoutrosLab.plotting.general 5.8.2 2017-08-11

BUG FIX

  • Completely reworked how spacing works in multipanel plot -- now creates rectangular grobs instead of using top/left/right/bottom padding

BoutrosLab.plotting.general 5.8.1 2017-08-11

BUG FIX

  • Multipanel plot background colour
  • Multipanel plot not accepting expression labels
  • Multipanel deleting plots main labels
  • heatmap legend layout works properly now

BoutrosLab.plotting.general 5.8.0 2017-08-11

ADDITIONS

  • new create.multiplot function (create.multipanelplot)

BUG FIX

  • auto-axis now gives 5 labels by default instead of 4
  • same.as.matrix can now be applied to create dendrogram outside of heatmap
  • fixed filename error in crete.gif
  • heatmap now loads defaults
  • segplot defaults to bold like rest of plots
  • colours for default dotmap now match the documentation (had to reverse them)

FEATURE UPDATE *pcawg.colours: new and renamed tumour type names added to palette, sv class 'insertion' assigned colour


BoutrosLab.plotting.general 5.7.6 2017-08-11

BUG FIX

  • 1D heatmaps now work -- automatically
  • Error bars now work properly with grouped bar plots

FEATURES

  • automatic layout justification for legends (using just arg) for continous legends
  • added helper function for seperating thousands by commas, i.e -> (12345) -> (12,345)
  • merged all the relevent colour functions into force.colour.scheme
  • can now extract dendrograms from a heatmap (only one, and may require manual manipulation)

BUG FIX

  • create.heatmap - grid row/column limits reversed
  • legend.grob - continuous legends produce warnings
  • ytop.rectangle in create.scatterplot() doesn't work properly.
  • Remove the old option (retrieve.plot.labels) and merge into (plot.labels.to.retrieve)

FEATURES

  • merged multiple colour functions (old ones to be removed in next commit)
  • multiple colours of error bars in scatterplot
  • Add xaxis.rot.top option to create.multiplot
  • have legends on both the left AND the right for create.heatmap

BoutrosLab.plotting.general 5.7.4 2017-07-19

BUG FIX

  • Automatic labels not working for stacked barplots
  • removed log scaling from stacked barplots
  • fixed 1 D heatmap issues

ADDITIONS

  • search metadata function

BoutrosLab.plotting.general 5.7.3 2017-06-06

FEATURE UPDATE

  • each plot can put xat/yat = "auto"/"auto.linear"/"auto.log" to get automatic labels

ADDITIONS

  • pretty axis function -- input data set gives updated data values and labels

BoutrosLab.plotting.general 5.7.2 2017-05-17

FEATURE UPDATE

  • Can now add border to correlation keys
  • Issues around multiplot reseting labels on y axis when x asis labels added solved

ADDITIONS

  • create.gif for creating animated plots

BoutrosLab.plotting.general 5.7.1 2017-05-17

BUG FIX

  • write.plot.R: fixed an error that didn't allow adding additional plots when returning object to screen (when filename = NULL)
  • create.barplot.R: fixed a bug interfering with add.rectangle and removed redundant add.background.shading (repeats add.rectangle functionality)
  • force.colour.scheme: if multiple outputs were requested only one would be returned; now returns a list

FEATURE UPDATE

  • create.barplot.R: minor improvements to some examples *split argument lwd into axes.lwd and border.lwd to be consistent with other functions *removed argument remove.all.border.lines as this can now be accomplished with axes.lwd

MINOR (FORMATTING) CHANGES

  • colour.gradient.R, covariates.grob.R, create.barplot.R, create.boxplot.R, create.colourkey.R, create.dendrogram.R, create.densityplot.R, create.hexbinplot.R, create.segplot.R, create.stripplot.R, create.violinplot.R, default.colours.R, display.colours.R, display.statistical.result.R, force.colour.scheme.R, generate.at.final.R, get.corr.key.R, get.defaults.R, get.line.breaks.R, legend.grob.R, scientific.notation.R, show.available.palettes.R, write.metadata.R, write.plot.R: applied code formatting (BL standards)

BoutrosLab.plotting.general 5.7.0 2017-05-11

BUG FIX

  • create.violinplot: fixed a bug in colour functionality; now repeats colours when fewer colours are supplied than there are groups

FEATURE UPDATE

  • create.hexbinplot: changed argument abline.type to abline.lty to be consistent with other functions
  • create.segplot: added warning for specific use case (multiplot fails when a vertical segplot is the first plot)
  • create.manhattanplot: changed argument axis.lwd to axes.lwd to be consistent with other functions

MINOR (FORMATTING) CHANGES

  • create.hexbinplot, create.histogram, create.manhattanplot, create.polygonplot, create.qqplot.comparison, create.qqplot.fit, create.scatterplot, create.stripplot, create.segplot, create.violinplot, age.categorical.colour, append.footnote: applied code formatting (BL standards)

BoutrosLab.plotting.general 5.6.24 2017-04-20

FEATURE UPDATE *create.multiplot: Added functionality to add top x-axis tick labels. Has not been extensively tested.


BoutrosLab.plotting.general 5.6.23 2017-02-09

BUG FIX *pcawg.colours: fixed bug that prevented project code colours from being returned.


BoutrosLab.plotting.general 5.6.22 2017-02-09

FEATURE UPDATE *create.dotmap: addition of parameters for rectangle border thickness, rectangle border colour.


BoutrosLab.plotting.general 5.6.21 2017-01-30

BUG FIX

  • create.scatterplot: adding conditional for when pch is not referring to a point (this is in reference to KM plots)

BoutrosLab.plotting.general 5.6.20 2017-01-28

FEATURE UPDATE

  • create.scatterplot: addition of parameter "col.border". This allows customizable border colours when pch >= 21.

BoutrosLab.plotting.general 5.6.19 2016-12-06

FEATURE UPDATE

  • pcawg.colours: add project.code to colour.schemes

BoutrosLab.plotting.general 5.6.18 2016-11-23

FEATURE UPDATE

  • create.polygonplot: option to add rectangles.

BoutrosLab.plotting.general 5.6.17 2016-11-08

FEATURE UPDATE

  • pcawg.colours: consistent colour palette for use on pcawg data

BoutrosLab.plotting.general 5.6.15 2016-10-24

FEATURE UPDATE

  • create.heatmap: rotation of the top x axis labels is now independent from the bottom x axsis labels.
  • create.multiplot: options to set the distance between tick marks and tick labels

BoutrosLab.plotting.general 5.6.14 2016-10-05

FEATURE UPDATE

  • create.polygonplot: option to add text.

BoutrosLab.plotting.general 5.6.13 2016-09-28

FEATURE UPDATE

  • create.polygonplot: added parameters alpha and median.lwd.

BoutrosLab.plotting.general 5.6.12 2016-09-07

FEATURE UPDATE

  • create.densityplot & create.violinplot: allow adjustment of bandwidth with parameters bandwidth and bandwidth.adjust.

BoutrosLab.plotting.general 5.6.11 2016-08-31

FEATURE UPDATE

  • create.stripplot: allow different border colour for added points when pch >= 21

BoutrosLab.plotting.general 5.6.10 2016-07-27

BUG FIX

  • reintegrated untagged changes to trunk and re-added scatterplot feature updates.

BoutrosLab.plotting.general 5.6.9 2016-07-25

FEATURE UPDATE

  • create.scatterplot: allow different border colour for added points when pch >= 21

BoutrosLab.plotting.general 5.6.8 2016-05-27

FEATURE UPDATE

  • create.dotmap: Added parameters 'columns' and 'rows' for spot.colour.function to allow dots colours to be grouped by columns or rows, respectively [BPG-16]. There are 12 distinct colours (the default colours) and the colours start to repeat when there are more than 12 columns/rows. It also checks that the columns/rows (depending on which side is selected) are unique and throws and error if they are not.

BoutrosLab.plotting.general 5.6.7 2016-05-19

BUG FIX

  • create.multiplot: fixed bug where NULL values in parameter list (for xlimits=/ylimits=) were being ignored/unprocessed [BPG-2].

BoutrosLab.plotting.general 5.6.6 2016-04-29

FEATURE UPDATE

  • create.barplot: Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' to allow users to add text labels to plot area. Added parameter 'box.ratio' for adjusting thickness of each bar. Added parameter 'remove.all.border.lines' to allow barplots with no borders. Added example for adding text to plot and adjusting box.ratio.

BUG FIX

  • create.barplot: fixed adding error bars for data-frames [BPG-4]

BoutrosLab.plotting.general 5.6.5 2016-04-27

MINOR UPDATE

  • create.boxplot: Added example for adding text to plot.
  • create.hexbinplot: Added example of stratified multiplot.

BoutrosLab.plotting.general 5.6.4 2016-04-21

FEATURE UPDATE

  • create.dotmap: NA plotting character can be made different colours with new variable, NA.spot.size.colour. Default is set to black.

BoutrosLab.plotting.general 5.6.2 2016-04-08

FEATURE UPDATE

  • get.cor.key: parameterizing number of decimal places to keep for spearman, pearson and kendall correlation values

BoutrosLab.plotting.general 5.4.3 2016-01-04

BUG FIXES: Inconsitency in dotmap/heatmap grid lines location fixed -> everything follows heatmaps spec now fixed bug where sample.order would reorde barplots incorrectly when horizontal default font sizes are consistent now default font sizes are more porportional

FEATURE UPDATES: ability to add multiple violin fill colours able to completely remove borders from heatmaps add p values automatically to box plots ability to set a sperate set of defaults based on type of publication ( default sets still need to be added) ability to pick what plots to retrieve plot labels from in create.multiplot


BoutrosLab.plotting.general 5.4.2 2015-12-22

FEATURE UPDATE:

  • create.scatterplot: added option to specify colour of grid lines.

BoutrosLab.plotting.general 5.3.9 2015-10-01

FEATURE UPDATE:

  • create.heatmap: turns off grid lines when row or column number exceeds a certain threshold.
  • auto-removal of grid lines can be overrided with forcing parameters

BoutrosLab.plotting.general 5.3.7

BUG FIXES: same.as.matrix will now correcting readjust label specifications when combining scatterplots, they will no longer only use error bars from one scatter plot yaxis.covariates parameter can now allow specific location specification so it does not overlap the heatmap xgrid.at and ygrid.at now properly update for all functions background rectangles are now drawn in the background instead of foreground when combining scatterplots, they will no longer only use the text specified from one scatter plot removed circular definitions from Rd files standardized parameter defaults

FEATURE UPDATES: Can now add subtitles through use of xaxis.top parameters Can now input a vector of files to be output to Can now sort boxes in create.boxplot by max, min, mean and median (defaults to median if not set) Can now draw both bands and lines on segplots Polygon plot will now auto-calculate x and y limits if not specified Can now vertically align labels and adjust there coordinates manually

BoutrosLab.plotting.general 5.3.4 2015-07-31

MINOR UPDATE:

  • create.scatterplot: updated ROC example to use auto-label placement

BoutrosLab.plotting.general 5.3.3 2015-07-28

MINOR UPDATE:

  • functions containing the word 'colour' now accept both American and Canadian spelling

BoutrosLab.plotting.general 5.3.2 2015-07-24

BUG FIXES:

  • create.heatmap: fixed bug which made labels disappear when stratifying dendrogram

BoutrosLab.plotting.general 5.3.1 2015-07-24

MINOR UPDATE:

  • minor updates to the plotting guide

BoutrosLab.plotting.general 5.3.0 2015-07-23

MINOR UPDATE:

  • standardized parameter names across all plotting functions
  • create.hexbinplot: added add.xyline and add.curves functionality (same as in create.scatterplot)

BoutrosLab.plotting.general 5.2.20 2015-07-13

MINOR UPDATE:

  • create.barplot, create.boxplot, create.hexbinplot, create.manhattanplot, create.polygonplot, create.scatterplot, create.segplot, create.stripplot, create.violinplot: Set xlab.label and ylab.label to default to formula components
  • default.colours: greyscale check no longer runs if only one colour is requested

BoutrosLab.plotting.general 5.2.19 2015-07-03

MINOR UPDATE:

  • force.colour.scheme: added snv colour scheme

BoutrosLab.plotting.general 5.2.18 2015-07-03

MINOR UPDATE:

  • Standardized all plotting functions to have resolution set to 1600 dpi
  • force.colour.scheme: Added spaces in appropriate tissue names

BoutrosLab.plotting.general 5.2.17 2015-06-16

MINOR UPDATE:

  • removed out-of-date comments from examples

BoutrosLab.plotting.general 5.2.16 2015-06-15

MINOR UPDATE:

  • re-created PlottingGuide to use revamped show.available.palettes function

BoutrosLab.plotting.general 5.2.13 2015-05-08

MINOR UPDATE

  • create.multiplot: added example showing how to save parameter options from individual plots

BoutrosLab.plotting.general 5.2.12 2015-05-07

MINOR UPDATE

  • create.heatmap: Added two parameters: text.position and text.offset to customize placement of text in cells
  • show.available.palettes: changed display of specific schemes to call create.heatmap (more robust method)

BoutrosLab.plotting.general 5.2.10 2015-04-22

BUG FIXES

  • show.available.palettes: fixed 'general' program to no longer introduces NAs by coersion

BoutrosLab.plotting.general 5.2.9 2015-04-21

MINOR UPDATE

  • create.hexbinplot: added comment to explain maxcnt removing datapoints from example plot

BoutrosLab.plotting.general 5.2.8 2015-03-12

MINOR UPDATE

  • create.barplot: allow vector of custom sorting order for samples
  • create.multiplot: has flag to remove all border lines from plots

BoutrosLab.plotting.general 5.2.6 2014-12-24

MINOR UPDATE

  • write.plot: fixed bug
  • added new colourkey legend and interface

BoutrosLab.plotting.general 5.2.5 2014-12-18

MINOR UPDATE

  • updated plotting guide to have more examples and slight wording adjustments

BoutrosLab.plotting.general 5.2.4 2014-12-16

MINOR UPDATE

  • create.barplot: ablines now appear in the background of the plot instead of the foreground

BoutrosLab.plotting.general 5.2.2 2014-12-09

MINOR UPDATE

  • write.plot: Added embed.plot functionality (depreciating said function)
  • embed.plot: Removed embed.plot()

BoutrosLab.plotting.general 5.2.1 2014-11-05

MINOR UPDATE

  • force.colour.scheme: Bug fix for annovar colour schemes

BoutrosLab.plotting.general 5.2.0 2014-10-17

MINOR UPDATE

  • Added `Nature' style option to all plotting functions

BoutrosLab.plotting.general 5.1.9 2014-10-16

MINOR UPDATE

  • create.scatterplot: for add.line.segments, changed line-end style to 'butt'
  • create.stripplot: NEW ARGUMENTS to allow for addition of lines showing group medians

BoutrosLab.plotting.general 5.1.7 2014-10-10

MINOR UPDATE

  • default.colours: added new schemes spiral.noon and spiral.night
  • default.colours: rearranged order of qual scheme to decrease red-green combinations
  • force.colour.scheme: changed CNV colours to red/blue/green/white, MSI to green/yellow, risk to red/yellow
  • reorganized default.colours and force.colour.scheme to return deprecated schemes
  • show.available.palettes: reorganized layout of 'specific' scheme output

BoutrosLab.plotting.general 5.1.6 2014-10-08

MINOR UPDATE

  • create.boxplot: added arguments to allow for addition of stripplot in background

BoutrosLab.plotting.general 5.1.5 2014-09-19

MINOR UPDATE

  • show.available.palettes: added new function to show schemes available in default.colours and force.colour.scheme
  • default.colours: refactored, changed greyscale warning to auto-calculate

BoutrosLab.plotting.general 5.1.4 2014-09-08

MINOR UPDATE

  • create.scatterplot: changed argument name - add.lines > add.line.segments
  • create.scatterplot: updated to accept lists of line segments to add

BoutrosLab.plotting.general 5.1.3 2014-08-22

MINOR UPDATE

  • PlottingGuide: converting to use knitr, added further details and references to design portion
  • MultiPlotTutorial: deleted, contents migrated to PlottingGuide

BoutrosLab.plotting.general 5.1.2 2014-08-14

MINOR UPDATE

  • create.manhattanplot: Updated documentation to use chromosome palette in force.colour.scheme

BoutrosLab.plotting.general 5.1.1 2014-08-14

MINOR UPDATE

  • create.barplot: changed default fill colour to black (instead of grey)

BoutrosLab.plotting.general 5.1.0 2014-08-12

MINOR UPDATE

  • create.scatterplot: NEW ARGUMENTS text.guess.* now allows users to specify data points so that associated label positions can be automatically determined
  • inside.rectangle: NEW FUNCTION which determines if a set of data points are inside a set of defined rectangles
  • inside.ellipse: NEW FUNCTION which determines if a set of data points are inside a set of defined ellipses

BoutrosLab.plotting.general 5.0.28 2014-08-08

MINOR UPDATE

  • Updated plotting guide to have extended design advice: added sections on resolution, file types, etc

BoutrosLab.plotting.general 5.0.27 2014-07-31

MINOR UPDATE

  • Updated examples in scatterplot, qqplot comparison, hexbinplot, heatmap, dotmap, and barplot to have better formatted axes labels

BoutrosLab.plotting.general 5.0.26 2014-07-31

BUG FIX

  • re-added argument line.lwd in create.scatterplot

BoutrosLab.plotting.general 5.0.25 2014-07-31

MINOR UPDATE

  • create.heatmap: NEW ARGUMENT gridline.order now allows user to specify in which order gridlines should be drawn (horizontal or vertical first)

BoutrosLab.plotting.general 5.0.24 2014-07-31

MINOR UPDATE

  • adjusted examples in qqplot.comparison, qqplot.fit and scatterplot to use character values for panel groupings

BoutrosLab.plotting.general 5.0.23 2014-07-30

MINOR UPDATE

  • display.colours now additionally displays names of colours

BUG FIX

  • added 'eye' to the 'tissue' palette in force.colour.scheme

BoutrosLab.plotting.general 5.0.22 2014-07-29

MINOR UPDATE

  • Fixed: create.scatterplot, add.lines now works with lists of data

BoutrosLab.plotting.general 5.0.20 2014-07-24

MINOR UPDATE

  • Changed multiplot example to use matching gene data

BoutrosLab.plotting.general 5.0.19 2014-07-23

MINOR UPDATE

  • Changing chromosome palette in force.colour.scheme to use more visually distinct colours

BoutrosLab.plotting.general 5.0.18 2014-07-23

BUG FIX

  • Changed datasets keep common genes among datasets

BoutrosLab.plotting.general 5.0.17 2014-07-21

MINOR UPDATE

  • Updated multiplot tutorial with new examples using generate data

BoutrosLab.plotting.general 5.0.16 2014-07-16

BUG FIX

  • default.colours: properly return the requested number of colours when multiple palettes requested

BoutrosLab.plotting.general 5.0.15 2014-07-11

MINOR UPDATE

  • create.scatterplot:
    • NEW ARGUMENTs allow for addition of line segments to be drawn BUG FIX
  • get.corr.key: fixed corner definition determined by x.pos and y.pos

BoutrosLab.plotting.general 5.0.14 2014-07-07

MINOR UPDATE

  • create.scatterplot:
    • NEW ARGUMENT allows for specification of strip title fontface
  • create.stripplot:
    • NEW ARGUMENT allows for specification of strip title fontface

BoutrosLab.plotting.general 5.0.11 2014-07-04

MINOR UPDATE

  • added example to create.dotmap clustered by dots and dendrogram added

BoutrosLab.plotting.general 5.0.10 2014-07-04

MINOR UPDATE

  • renamed colour schemes in default.colours to follow spiral. format

BoutrosLab.plotting.general 5.0.10 2014-07-04

MINOR UPDATE

  • added biomolecule colour scheme to force.colour.schemes
  • migrated chromosome colour scheme to force.colour scheme from default.colours
  • renamed extra colour schemes in default.colours

BoutrosLab.plotting.general 5.0.9 2014-07-03

MINOR UPDATE

  • formatting adjustments to examples

BoutrosLab.plotting.general 5.0.8 2014-07-03

MINOR UPDATE

  • changed SNV dataset numerical coding to be simpler

BoutrosLab.plotting.general 5.0.7 2014-07-02

BUG FIXES

  • palettes in default.colours function properly return subsets

BoutrosLab.plotting.general 5.0.6 2014-06-13

MINOR UPDATE

  • force.colour.scheme now accepts both upper and lower case input

BoutrosLab.plotting.general 5.0.5 2014-06-11

MINOR UPDATE

  • Changed default sequential, diverging, and binary schemes

BoutrosLab.plotting.general 5.0.4 2014-06-10

MINOR UPDATE

  • Added more schemes to default.colours

BoutrosLab.plotting.general 5.0.3 2014-06-04

MINOR UPDATE

  • Added plotting guide to vignettes

BoutrosLab.plotting.general 5.0.2 2014-06-02

BUG FIXES

  • create.barplot:
    • Re-added origin to panel call to allow for negative bars
    • Set y-axis default values to appear automatically
    • Fixed ordering of bars by increasing data
  • create.histogram: Silenced warning caused by data parameter

BoutrosLab.plotting.general 5.0.1 2014-06-02

MINOR UPDATE

  • force.colour.scheme: Added colour schemes in addition to the 'annovar' schemes
  • default.colours: Added additional 5-colour palette

BoutrosLab.plotting.general 5.0.0 2014-05-29

MAJOR UPDATE

  • create.scatterplot.with.error: Removed function, merged with create.scatterplot
  • panel.BL.bwplot: Removed function, functionality no longer needed
  • create.multiple.stripplots: Removed function, functionality contained within create.stripplot
  • create.multiple.boxplots: Removed function, functionality contained within create.boxplot
  • create.barplot.with.error: Removed function, functionality contained within create.barplot
  • rgb.to.greyscale: Removed function, moved into display.colours
  • colour.to.grey: Removed function, moved into display.colours
  • scientific.notation.2: Removed function, functionality contained within scientific.notation
  • scientific.notation.expr: Removed function, functionality contained within scientific.notation
  • create.violinplot: Renamed function from create.violin.plot
  • create.polygonplot: Renamed function from create.polygon

MINOR UPDATE

  • Code and documentation base reviewed to match lab formatting standard
  • Updating examples in documentation to use standard datasets instead of fake data
  • create.multiplot: Updated example plots to use standard dataset
  • patient: Added additional data to show proportions of base changes
  • create.scatterplot: Added example using error bars
  • scientific.notation: Now returns either an expression or list
  • Updated test-suite to save a single multiplot to file

BoutrosLab.plotting.general 4.3.14 2014-05-28

MINOR UPDATE

  • Updated test suite to remove soon-to-be deleted plotting functions

BoutrosLab.plotting.general 4.3.13 2014-05-23

MINOR UPDATE

  • Formatted examples in documentation to contain less than 100 characters per line
  • SNV: changed encoding of dataset to use numerical values instead of character values

BoutrosLab.plotting.general 4.3.12 2014-05-22

MINOR UPDATE

  • create.violin.plot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.11 2014-05-22

MINOR UPDATE

  • create.stripplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.10 2014-05-22

MINOR UPDATE

  • create.stripplot: Exposing xat and xlimits parameter to allow for customization of horizontal plots

BoutrosLab.plotting.general 4.3.9 2014-05-22

MINOR UPDATE

  • create.segplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.8 2014-05-21

MINOR UPDATE

  • create.scatterplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.7 2014-05-21

MINOR UPDATE

  • Removed old datasets and updated documentation examples to use newly formatted data
  • Set LazyData in DESCRIPTION to 'yes' so that datasets can be referenced by name alone

BoutrosLab.plotting.general 4.3.6 2014-05-21

MINOR UPDATE

  • CNA, SNV, microarray, patient: Added new datasets to data/ folder, each with a corresponding Rd file
  • Deleted old 'p value' dataset formerly used for create.manhattanplot examples

BoutrosLab.plotting.general 4.3.5 2014-05-21

MINOR UPDATE

  • create.colourkey: Fixed formatting in documentation to fit under 90 characters per line
  • create.histogram: Updated example code to check dataset size instead of use hard-coded values
  • microarray: Decreased size of microarray dataset

BoutrosLab.plotting.general 4.3.4 2014-05-20

MINOR UPDATE

  • create.colourkey: Exposed parameter for colourkey cex

BoutrosLab.plotting.general 4.3.3 2014-05-20

MINOR UPDATE

  • create.qqplot.fit: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.2 2014-05-20

MINOR UPDATE

  • create.qqplot.comparison: Updated example plots to use standard dataset
  • MultiPlotTutorial: Reduced file size

BoutrosLab.plotting.general 4.3.1 2014-05-19

MINOR UPDATE

  • create.polygon: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.3.0 2014-05-16

MINOR UPDATE

  • run_plots: Added test script to package

BoutrosLab.plotting.general 4.2.40 2014-05-16

MINOR UPDATE

  • create.histogram: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.39 2014-05-16

MINOR UPDATE

  • create.hexbinplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.38 2014-05-16

MINOR UPDATE

  • create.dotmap: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.37 2014-05-15

MINOR UPDATE

  • create.densityplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.36 2014-05-15

MINOR UPDATE

  • create.boxplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.35 2014-05-15

MINOR UPDATE

  • create.heatmap: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.34 2014-05-15

BUG FIXES

  • create.heatmap: Fixed error where heatmap threw error if symbols were added, but not 'border' symbols

BoutrosLab.plotting.general 4.2.33 2014-05-15

MINOR UPDATE

  • create.heatmap: Added clarification to documentation that 'colour.alpha' can be set to 'automatic'
  • create.multiplot: Expose parameters for x-axis and y-axis tick mark lengths

BoutrosLab.plotting.general 4.2.32 2014-05-14

MINOR UPDATE

  • create.violinplot: Removed error message for using pch>=21 with lattice version 20-13
  • create.violinplot: Modified handling of border and fill colours for extra points

BoutrosLab.plotting.general 4.2.31 2014-05-13

MINOR UPDATE

  • create.manhattanplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.30 2014-05-12

MINOR UPDATE

  • create.barplot: Updated example plots to use standard dataset

BoutrosLab.plotting.general 4.2.29 2014-05-12

MINOR UPDATE

  • create.dotmap: enabled default behaviour for NA values to plot 'X' characters size 7

BoutrosLab.plotting.general 4.2.28 2014-05-12

MINOR UPDATE

  • create.dotmap: Improved handling of multiple pch with multiple fill colours

BoutrosLab.plotting.general 4.2.27 2014-05-08

MINOR UPDATE

  • create.dotmap: Deleted warning for using pch>=21 with lattice version 20-13 (outdated)

BoutrosLab.plotting.general 4.2.26 2014-05-02

MINOR UPDATE

  • create.dotmap: Stopped printing of warning regarding using pch>=21 with lattice version 20-13

BoutrosLab.plotting.general 4.2.25 2014-04-25

MINOR UPDATE

  • Fixed spelling errors in documentation and code

BoutrosLab.plotting.general 4.2.24 2014-04-24

MINOR UPDATE

  • embed.plot: Added example & updated documentation to use proper parameters
  • create.hexbinplot: Fixed formatting issue
  • create.scatterplot: Fixed auto-sensing of labels
  • create.barplot: Added functionality of adding text above bars
  • create.heatmap: Added ability to have multi-sized borders
  • create.heatmap: Adjusted input of 'main' to accept non-list values
  • MultiPlotTutorial: Compressed pdf
  • Updated formatting of all function documentation
  • NAMESPACE: Added imports

BoutrosLab.plotting.general 4.2.23 2014-04-17

MINOR UPDATE

  • create.densityplot: Added data-sensing
  • create.scatterplot: Added data-sensing
  • create.hexbinplot: Added example of multi-colour scheme

BoutrosLab.plotting.general 4.2.22 2014-04-17

MINOR UPDATE

  • create.densityplot: Expose top, bottom, left, and right padding parameters
  • create.hexbinplot: Expose top, bottom, left, and right padding parameters
  • create.qqplot.fit: Expose top, bottom, left, and right padding parameters
  • create.qqplot.comparison: Expose top, bottom, left, and right padding parameters
  • create.violin.plot: Expose top, bottom, left, and right padding parameters
  • create.heatmap: Added removal of top bar in stratified dendrograms

BUG FIXES

  • Fixed bugs, typos, and mismatches in multiplot tutorial sample code
  • create.heatmap: Fixed coding issues

BoutrosLab.plotting.general 4.2.21 2014-04-13

MINOR UPDATE

  • embed.plot: Added new function to allow for plot-within-a-plot layouts

BoutrosLab.plotting.general 4.2.20 2014-04-13

MINOR UPDATE

  • create.heatmap: Added ability to automatically estimate values for colour.alpha parameter
  • create.heatmap: Added example for automatic colour.alpha value estimation

BUG FIXES

  • create.heatmap: Fixed grid to also draw lines on first row & column
  • create.barplot: Fixed default units to inches
  • create.heatmap: Fixed documentation to match changes in code
  • create.boxplot: Fixed naming issue
  • create.multiplot: Fixed naming conventions

BoutrosLab.plotting.general 4.2.19 2014-04-04

MINOR UPDATE

  • Added new function 'colour.gradient' to generate sequential colour palettes

BoutrosLab.plotting.general 4.2.18 2014-03-31

MINOR UPDATE

  • create.heatmap: Added ability to stratify dendrogram
  • create.boxplot: Added ability to reorder boxplots based on median values

BoutrosLab.plotting.general 4.2.17 2014-03-26

MINOR UPDATE

  • create.barplot: Added ability to draw curves
  • create.boxplot: Added ability to draw curves
  • create.barplot.with.error: Adjusted whisker length to not cover whole bar
  • create.heatmap: Added example of per-cell font characteristics
  • create.barplot: Added example of grouped labels
  • create.boxplot: Added option of drawing line either in front of or behind plot

BUG FIXES

  • create.heatmap: Fixed issue with symbols

BoutrosLab.plotting.general 4.2.16 2014-03-17

MINOR UPDATE

  • create.heatmap: Added global covariate outline
  • create.barplot: Added grouping of labels for grouped barplot
  • create.heatmap: Added examples
  • create.multiplot: Added examples

BUG FIXES

  • write.metadata: Fixed to stop printing warnings

BoutrosLab.plotting.general 4.2.15 2014-03-14

MINOR UPDATE

  • create.multiplot: Added ability to retrieve plot labels & limits from 'original' plots
  • create.multiplot: Updated examples

BUG FIXES

  • scientific.notation.expr: Fixed issue & code formatting
  • write.metadata: Fixed issue with dependencies

BoutrosLab.plotting.general 4.2.14 2014-03-05

MINOR UPDATE

  • create.heatmap: Added functionality of inserting additional symbols
  • create.heatmap: Added example to documentation of symbol usage
  • create.scatterplot: Changed ablines to be drawn in front of plot
  • Added datasets files to inst folder for later use in examples
  • Added vignettes folder containing multiplot tutorial

BUG FIXES

  • create.barplot: Fixing reordering of bars

BoutrosLab.plotting.general 4.2.13 2014-02-26

MINOR UPDATE

  • create.barplot: Set default reordering to FALSE
  • create.dotmap: Added functionality to change dot colour

BoutrosLab.plotting.general 4.2.12 2014-02-25

MINOR UPDATE

  • create.barplot: Added functionality to reorder bars to be increasing or decreasing
  • create.hexbinplot: Added more examples
  • Exposed 'fontface' parameter in all plotting functions

BoutrosLab.plotting.general 4.2.11 2014-02-23

MINOR UPDATE

  • display.statistical.result: Updated defaults in documentation

BoutrosLab.plotting.general 4.2.10 2014-02-06

MINOR UPDATE

  • create.hexbinplot: Added background colour
  • create.hexbinplot: Added ability to have tick marks on top x axis only
  • create.hexbinplot: Enabled svg output
  • create.hexbinplot: Added examples to documentation

BUG FIXES

  • create.barplot: Removed origin from panel call to enable creation of stacked, horizontal, unidirectional plots

BoutrosLab.plotting.general 4.2.9 2014-02-03

MINOR UPDATE

  • display.statistical.result: Added option to change ":" to a different symbol
  • create.hexbinplot: Added ability to change background colour
  • create.heatmap: Added ability to display tick marks on top axis only
  • Enabled svg output for all plots

BoutrosLab.plotting.general 4.2.8 2014-01-27

MINOR UPDATE

  • Re-added package

BoutrosLab.plotting.general 4.2.7 2014-01-10

MAJOR UPDATE

  • Added create.manhattanplot function

BoutrosLab.plotting.general 4.2.4 2013-11-22

MINOR UPDATE

  • Added TODO file

BoutrosLab.plotting.general 4.2.3 2013-11-18

MINOR UPDATE

  • create.boxplot: Added ability to draw rectangle panels
  • create.boxplot: Added new example with grey shading between different boxes

BoutrosLab.plotting.general 4.2.2 2013-11-13

MINOR UPDATE

  • create.barplot: Added ability to change the width of the box

BoutrosLab.plotting.general 4.2.1 2013-11-13

MINOR UPDATES

  • create.barplot: Added new parameters - background.col and draw.grid
  • create.barplot: Added new example of grey background with white grid lines

BoutrosLab.plotting.general 4.2.0 2013-11-12

MINOR UPDATE

  • default.colours: Changed default qualitative palette to have brighter colours, and 12 options instead of only 9. Previous qualitative palette still accessible by setting palette.type = 'old.qual'

BoutrosLab.plotting.general 4.1.8 2013-11-11

MINOR UPDATES

  • default.colours: Removed deprecated survival colour scheme
  • Changed warning about greyscale compatibility to be more general

BoutrosLab.plotting.general 4.1.7 2013-11-11

MINOR UPDATES

  • default.colours: Removed deprecated old chromosome colour scheme
  • Replaced 'sandybrown' with 'tan1' in new chromosome palette

BoutrosLab.plotting.general 4.1.6 2013-11-11

MINOR UPDATE

  • Added create.colourkey to NAMESPACE

BoutrosLab.plotting.general 4.1.5 2013-11-10

MINOR UPDATE

  • Update and reorder NAMESPACE

BoutrosLab.plotting.general 4.1.4 2013-11-09

MINOR UPDATE

  • Removed unnecessary requires in get.corr.key

BoutrosLab.plotting.general 4.1.3 2013-11-09

MINOR UPDATE

  • Updated minimum required versions of dependencies

BoutrosLab.plotting.general 4.1.2 2013-11-09

MINOR UPDATES

  • create.barplot: Updated manual to reflect addition of 'axis.fontface' argument
  • create.colourkey: Removed 'enable.warnings' argument

BoutrosLab.plotting.general 4.1.1 2013-11-08

MINOR UPDATE

  • create.barplot: Added arguments 'xaxis.fontface' and 'yaxis.fontface'

BoutrosLab.plotting.general 4.1.0 2013-11-05

MAJOR UPDATE

  • Added new function: 'create.colourkey' to generate and draw colourkey

BoutrosLab.plotting.general 4.0.7 2013-11-04

MINOR UPDATES

  • create.stripplot: New arguments 'xaxis.fontface', 'yaxis.fontface' to allow for modification of axis tck label font face
  • create.stripplot: New argument 'ylab.axis.padding' allows for modification of padding between yaxis label and tck labels

BoutrosLab.plotting.general 4.0.6 2013-11-01

MINOR UPDATES

  • create.dendrogram: Updated documentation for jaccard usage
  • create.heatmap: Updated documentation for jaccard usage
  • create.heatmap: Moved logic for x.tck out of level plot

BoutrosLab.plotting.general 4.0.5 2013-10-25

MINOR UPDATES

  • create.heatmap: Refactoring and cleanup of code

BoutrosLab.plotting.general 4.0.4 2013-10-21

MINOR UPDATES

  • create.polygon: Added 'median.lty' (for seq power plot)

BoutrosLab.plotting.general 4.0.3 2013-10-18

MINOR UPDATES

  • create.hexbinplot: Changed default of 'mincnt' to 1 (from 0)

BoutrosLab.plotting.general 4.0.2 2013-09-26

MINOR UPDATES

  • create.scatterplot.with.error: New arguments to specify plot layout and placement - 'layout', 'as.table', 'x.spacing', 'y.spacing'
  • create.polygon: Added parameters 'axis.log' and 'yaxis.log'

BoutrosLab.plotting.general 4.0.1 2013-08-26

MINOR UPDATES

  • create.dotmap: Added example

BoutrosLab.plotting.general 4.0.0 2013-08-13

MAJOR UPDATES

  • Added 'write.metadata' function
  • Added 'description' parameter to all plotting function documentations
  • write.metadata: Added 'operating system', 'machine', 'system2'
  • create.multiplot: Updated documentation

BoutrosLab.plotting.general 3.10.2 2013-07-29

MINOR UPDATES

  • default.colours: Update chromosome colour scheme to be coded by letter-names rather than numbers, and using more easily-distinguished colours

BoutrosLab.plotting.general 3.10.1 2013-07-25

MINOR UPDATES

  • legend.grob: Added ability to specify size (width) of legend boxes for each legend individually

BoutrosLab.plotting.general 3.10.0 2013-07-25

MAJOR UPDATES

  • create.scatterplot: Added parameter 'axis.key.padding' to adjust spacing between y-axis and key
  • create.scatterplot: Added parameters 'add.points', 'points.x', 'points.y', 'points.col', 'points.pch', 'points.cex' - allow users to add additional points to plot area
  • create.scatterplot: Added parameters 'add.text', 'text.x', 'text.y', 'text.labels', 'text.col', 'text.cex', 'text.fontface' - allow users to add text labels to plot area

BoutrosLab.plotting.general 3.9.6 2013-07-25

MINOR UPDATES

  • create.dotmap: Added padding parameter

BoutrosLab.plotting.general 3.9.5 2013-07-19

MINOR UPDATES

  • create.barplot: Adjustments to spacing and commenting
  • create.dotmap: Added ability to specify padding on all sides of plot

BoutrosLab.plotting.general 3.9.4 2013-07-17

MINOR UPDATES

  • create.multiplot: New argument 'axes.lwd' to specify border line thickness

BoutrosLab.plotting.general 3.9.3 2013-07-15

MINOR UPDATES

  • create.multiplot: Fixed 'xlab.to.xaxis.padding' variable to change the correct parameter

BoutrosLab.plotting.general 3.9.2 2013-07-12

MINOR UPDATES

  • create.heatmap: Added ability to specify two x-axes, and gave meaning to 'x-alternating = 3' (prints tick marks on top and bottom x axes)
  • create.multiplot: Added 'xlab.to.xaxis.padding' parameter

BoutrosLab.plotting.general 3.9.1 2013-07-09

MINOR UPDATES

  • create.dotmap: Replaced 'grid.colour' with 'row.colour' and 'col.colour'
  • create.barplot: Updated to accept arguments that handle background shading
  • create.heatmap: Added 'xaxis.tck' and 'yaxis.tck' parameters to override default values based on covariate size

BoutrosLab.plotting.general 3.9.0 2013-07-04

MINOR UPDATES

  • create.multiplot: Added 'layout.skip' parameter to allow for blank spots in layout, and also added a complex example

BoutrosLab.plotting.general 3.8.7 2013-06-28

MINOR UPDATES

  • rgb.to.greyscale: Changing function to return results, rather than print

BoutrosLab.plotting.general 3.8.6 2013-06-27

MINOR UPDATES

  • append.footnote: Added function to create plot footnotes
  • default.colours: Fixed method of returning one-colour palettes for backwards compatibility

BoutrosLab.plotting.general 3.8.5 2013-06-17

MINOR UPDATES

  • default.colours: Adjustments to chromosome colour palette
  • default.colours: Added ability to provide multiple sequential and binary colour schemes

BoutrosLab.plotting.general 3.8.4 2013-06-13

MINOR UPDATES

  • create.boxplot: Added ability to define 'abline.v'

BoutrosLab.plotting.general 3.8.3 2013-06-12

MINOR UPDATES

  • display.colours: Added function to view colour palettes and what they look like in grey scale

BoutrosLab.plotting.general 3.8.2 2013-06-11

MINOR UPDATES

  • covariates.grob: Added 'reorder.grid.index' parameter to specify ordering of grid indices
  • create.heatmap: Added 'covariates.reorder.grid.index' and 'covariates.top.reorder.grid.index' parameters to match changes to covariates.grob

BoutrosLab.plotting.general 3.8.1 2013-06-10

MINOR UPDATES

  • create.heatmap: Split 'grid.colour' and 'grid.lwd' parameters into 'row.colour/col.colour' and 'row.lwd/col.lwd'
  • create.heatmap: Added grandfather parameters for 'grid.colour' and 'grid.lwd'

BoutrosLab.plotting.general 3.8.0 2013-06-04

MAJOR UPDATES

  • colour.to.grey: Added new function to convert R colours to R grey colours

BoutrosLab.plotting.general 3.7.0 2013-05-29

MAJOR UPDATES

  • create.heatmap: Added 'covariates.row.lines', 'covariates.col.lines', 'covariates.top.row.lines', 'covariates.top.col.lines' corresponding to new covariates.grob arguments, and updated examples
  • covariates.grob: Added parameters 'row.lines' and 'col.lines' to allow user to specify which grid lines to draw in covariate bars, and updated examples

BoutrosLab.plotting.general 3.6.20 2013-04-23

MINOR UPDATES

  • get.corr.key: New arguments to allow for the addition of a title to the key

BoutrosLab.plotting.general 3.6.19 2013-04-04

MINOR UPDATES

  • create.barplot: Attempting to make sizes match up
  • create.dotmap: Can now have custom colours specified
  • write.plot: Code formatting changes

BoutrosLab.plotting.general 3.6.18 2013-03-19

MINOR UPDATES

  • create.barplot: Code clean-up to match coding standards

BoutrosLab.plotting.general 3.6.17 2013-03-12

MINOR UPDATES

  • create.barplot: Fix to align error bars when barplot is grouped
  • write.plot: Refactor to place extension-specific code in inst/ext2function.txt

BoutrosLab.plotting.general 3.6.16 2013-03-07

MINOR UPDATES

  • write.plot: Allowing pdf and png output

BoutrosLab.plotting.general 3.6.15 2013-03-05

MINOR UPDATES

  • create.segplot: Added 'abline.h' parameter

BoutrosLab.plotting.general 3.6.14 2013-03-01

MINOR UPDATES

  • create.heatmap: Centralize parameter-checking code at start of script
  • Added pch>=21 warning to appropriate R files, and removed ^M

BoutrosLab.plotting.general 3.6.13 2013-02-19

MINOR UPDATES

  • create.polygon: Added line plotting options 'add.xyline', 'abline.h', 'abline.v'
  • create.barplot: Added examples

BoutrosLab.plotting.general 3.6.12 2013-02-14

MINOR UPDATES

  • create.multiplot: Added check for NAs in the legends workaround

BoutrosLab.plotting.general 3.6.11 2013-02-12

MINOR UPDATES

  • create.multiplot: Added workaround for lattice being unable to accept multiple legends with the same name via update.trellis
  • create.multiplot: Allowed x/y-relations between plots to be set

BoutrosLab.plotting.general 3.6.10 2013-02-06

MINOR UPDATES

  • create.multiplot: Added 'xlab.padding', and 'key.bottom.padding'
  • Added copyright header to R files

BoutrosLab.plotting.general 3.6.9 2013-01-30

MINOR UPDATES

  • create.barplot: Updating with "raster" command
  • create.multiplot: Making examples prettier, moving key.bottom.padding into argument

BoutrosLab.plotting.general 3.6.8 2013-01-30

MINOR UPDATES

  • create.barplot: Merging with create.barplot.with.error
  • create.barplot.with.error: Merging with create.barplot
  • create multiplot: Adding 'xaxis.fontface', 'yaxis.fontface' to allow for specification of axis-label fontface

BoutrosLab.plotting.general 3.6.7 2013-01-23

MINOR UPDATES

  • create.scatterplot: Added explicit horizontal argument
  • create.barplot: Added options to specify distance between x-axis and label
  • create.scatterplot: Add options to pass arbitrary plots onto lattice:xyplot
  • create.barplot.with.error: Fixing documentation
  • create.barplot: Allow user to edit 'key.bottom'
  • create.stripplot: Added parameters to allow for different border/fill colours (for pch 21:25), 'colour.alpha' to allow for plotting character transparencies, 'as.table', 'x.spacing', 'y.spacing' for customization of panels

BoutrosLab.plotting.general 3.6.6 2013-01-09

MINOR UPDATES

  • create.dotmap: Added argument 'pch.border.col' to set colour of dot border if pch is 21:25

BoutrosLab.plotting.general 3.6.5 2013-01-09

MINOR UPDATES

  • create.scatterplot: Added 'key.left.padding' parameter to place legends to left of graph
  • create.scatterplot: Added 'axes.lty' to set line style of axes lines
  • force.colour.scheme: Added another colour palette
  • create.multiplot: Added three parameters - 'xaxis.rot', 'key.left.padding', 'key.right.padding'

BoutrosLab.plotting.general 3.6.4 2012-12-14

MINOR UPDATES

  • create.heatmap: Added option of including x and y axis label covariates (between label and heatmap), and examples

BoutrosLab.plotting.general 3.6.3 2012-12-14

MINOR UPDATES

  • force.colour.scheme: Added alternative colour scheme for annovar output

BoutrosLab.plotting.general 3.6.2 2012-12-12

MINOR UPDATES

  • get.corr.key: Added missing else case for beta1.p
  • force.colour.scheme: Added synonymous SNV to the list

BoutrosLab.plotting.general 3.6.1 2012-12-11

MINOR UPDATES

  • create.multiplot: Changed key.left value to 1 so that legends can be placed to left of multiplot area

BoutrosLab.plotting.general 3.6.0 2012-12-11

MAJOR UPDATES

  • create.scatterplot: Added ability to draw rectangles in background

BoutrosLab.plotting.general 3.5.17 2012-12-09

MINOR UPDATES

  • create.polygon: Changed default values of 'xgrid.at' and 'ygrid.at'
  • create.polygon: Added 'xaxis.fontface' and 'yaxis.fontface'
  • create.polygon: Added 'fontface = xaxis.fontface' and 'fontface = yaxis.fontface' to scales$x and scales$y
  • create.polygon: Added example to demonstrate use with legend.grob

BoutrosLab.plotting.general 3.5.16 2012-12-08

MINOR UPDATES

  • create.polygon: Adjusted values of par.settings$layout.widths$axis.key.padding and par.settings$layout.heights$axis.key.padding to equal 1 - this lets the legend on the right be properly rendered

BoutrosLab.plotting.general 3.5.15 2012-12-07

MINOR UPDATES

  • create.barplot: Added ability to create horizontal barplots - 'plot.horizontal', 'xlimits', and 'xat' parameters added & example

BoutrosLab.plotting.general 3.5.14 2012-12-07

MINOR UPDATES

  • create.scatterplot: Fixing example to adjust placement of yaxis title
  • create.dotmap: Adding parameter 'fill.colour' to allow user to fill background of cells

BoutrosLab.plotting.general 3.5.13 2012-11-28

MINOR UPDATES

  • force.colour.scheme: Added overload functionality, changed scheme
  • Updating date with version

BoutrosLab.plotting.general 3.5.12 2012-11-28

MINOR UPDATES

  • force.colour.scheme: Added new force colour scheme function

BoutrosLab.plotting.general 3.5.12 2012-11-26

MINOR UPDATES

  • create.barplot: Added ability to draw vertical lines

BoutrosLab.plotting.general 3.5.11 2012-11-26

MINOR UPDATES

  • create.multiplot: Updated documentation to show to remove tick marks

BoutrosLab.plotting.general 3.5.10 2012-11-26

MINOR UPDATES

  • get.line.breaks: Added get line breaks function

BoutrosLab.plotting.general 3.5.9 2012-11-23

MINOR UPDATES

  • create.heatmap: Added check for features exceeding pixels/width

BoutrosLab.plotting.general 3.5.8 2012-11-23

MINOR UPDATES

  • create.polygon: Reverted functionality back to using if statements instead of ternary operators
  • create.heatmap: Added covariate bar between heatmap and xaxis labels

BoutrosLab.plotting.general 3.5.7 2012-11-13

MINOR UPDATES

  • create.dotmap: Added 'grid.col.lwd' and 'grid.row.lwd' to allow different weights of gridlines

BoutrosLab.plotting.general 3.5.6 2012-11-13

MINOR UPDATES

  • create.dotmap: Updated 'key.left', 'key.right', 'key.bottom' to default to 1 so that legends/keys are properly incorporated
  • create.dotmap: Added example using covariate bar and legend

BoutrosLab.plotting.general 3.5.5 2012-11-08

MINOR UPDATES

  • create.heatmap: Use grobPack() fontfamily specification to avoid unknown Arial font specification
  • create.dotmap: Changed yaxis label default to not be bold
  • legend.grob: Added parameters - 'layout', 'between.col', 'between.row' to allow user to specify layout for multiple legends and set empty space between rows/columns
  • legend.grob: Changed titles in legend to use a text grob instead of draw.key
  • create.heatmap: Added 'legend.layout', 'legend.between.col', and 'legend.between.row' parameters

BoutrosLab.plotting.general 3.5.4 2012-11-02

MINOR UPDATES

  • create.dotmap: Updated to use dotmap colour scheme by default, fixed palette creation for >3 colour schemes
  • create.dotmap: Added example with 5-colour background

BoutrosLab.plotting.general 3.5.3 2012-10-30

MINOR UPDATES

  • create.heatmap: Added set.seed() call at beginning of examples

BoutrosLab.plotting.general 3.5.2 2012-10-29

MINOR UPDATES

  • create.scatterplot: Fixed codoc error
  • General fixes for coding-style standardization and document fixes
  • Updates to dependency versions

BoutrosLab.plotting.general 3.5.1 2012-10-26

MINOR UPDATES

  • create.scatterplot: Changed default curves to use min/max with na.rm=T

BoutrosLab.plotting.general 3.5.0 2012-10-10

MAJOR UPDATES

  • covariates.grob: Added parameters 'grid.row', 'grid.col', 'grid.border' to allow customization of grid lines within covariate bars
  • create.heatmap: Added parameters 'covariates.grid.row', 'covariates.grid.col', 'covariates.grid.border', 'covariates.top.grid.row', 'covariates.top.grid.col', 'covariates.top.grid.border', 'legend.border', 'legend.border.padding'
  • create.heatmap: Added parameters 'covariates.padding', and 'covariates.top.padding' to allow for empty space between covariate bars and dendrograms
  • legend.grob: Added parameters 'border', 'border.padding' to allow for border around legend
  • Updated examples

BoutrosLab.plotting.general 3.4.4 2012-10-10

MINOR UPDATES

  • display.statistical.result: Added space before and after "x" sign

BoutrosLab.plotting.general 3.4.3 2012-10-10

MINOR UPDATES

  • create.heatmap: Changed 'grid.row' and 'grid.col' to default to false
  • create.heatmap: No longer assumes that matrices with less than 125 rows/columns should have grid lines

BoutrosLab.plotting.general 3.4.2 2012-10-02

MINOR UPDATES

  • display.statistical.result: Migrating this function to plotting.general

BoutrosLab.plotting.general 3.4.1 2012-09-25

MINOR UPDATES

  • create.heatmap: Added code to close devices opened by the grid::covertUnit function and remove Rplots.pdf files if necessary
  • legend.grob: Added code to remove Rplots.pdf files created by the lattice::draw.key

BoutrosLab.plotting.general 3.4.0 2012-09-12

MAJOR UPDATES

  • default.colours: Added gender colour palette
  • create.dendrogram: Interface change - renamed cluster.dimensions (pl.) to cluster.dimension (s.) because only takes scalars
  • create.dendrogram: Code clean-up
  • create.dendrogram: Fixed handling of jaccard distance

BoutrosLab.plotting.general 3.3.7 2012-09-10

MINOR UPDATES

  • create.segplot: Removed warning caused by typo in man file

BoutrosLab.plotting.general 3.3.6 2012-08-30

MINOR UPDATES

  • legend.grob: Added code to close extra device created by the draw.key()

BoutrosLab.plotting.general 3.3.5 2012-08-29

MINOR UPDATES

  • create.densityplot: Set groups to an ordered factor (avoids auto-alphabetical ordering by lattice during plotting)

BoutrosLab.plotting.general 3.3.4 2012-08-24

MINOR UPDATES

  • create.polygon: Added example

BoutrosLab.plotting.general 3.3.3 2012-08-20

MINOR UPDATES

  • create.segplot: Removed unused parameter from function definition & fixed inconsistencies

BoutrosLab.plotting.general 3.3.2 2012-08-20

MINOR UPDATES

  • create.boxplot: Replaced call to panel.BL.bwplot with call to panel.bwplot

BoutrosLab.plotting.general 3.3.1 2012-08-17

MINOR UPDATES

  • default.colours: Added new 2-colour scheme for dotmaps
  • create.dotmap: Updated example to use new dotmap colour scheme from default.colours

BoutrosLab.plotting.general 3.3.0 2012-08-17

MINOR UPDATES

  • create.segplot: Added new function to create segplots

BoutrosLab.plotting.general 3.2.31 2012-08-16

MINOR UPDATES

  • create.heatmap: Added notes in help file for using euclidean when lots of ties and correlation fails
  • legend.grob: Added notes in help file for using euclidean when lots of ties and correlation fails

BoutrosLab.plotting.general 3.2.30 2012-08-14

MINOR UPDATES

  • create.violinplot: Fixed a bug in extra points argument
  • create.scatterplot: Added alpha argument to control plotting transparency

BoutrosLab.plotting.general 3.2.29 2012-08-14

MINOR UPDATES

  • create.dendrogram: Updated to use dist(method = "jaccard") instead of jaccard.distance()

BoutrosLab.plotting.general 3.2.28 2012-08-07

MINOR UPDATES

  • default.colours: Changed warning message when survival colour scheme is used with more than 5 colours

BoutrosLab.plotting.general 3.2.27 2012-08-02

MINOR UPDATES

  • create.polygon: Fixed border.col argument to allow different coloured borders for multiple groups

BoutrosLab.plotting.general 3.2.26 2012-07-31

MINOR UPDATES

  • create.dendrogram: Changed jaccard.distance to use 't(x)' instead of 'x' in order to imitate behaviour of dist function

BoutrosLab.plotting.general 3.2.25 2012-07-26

MINOR UPDATES

  • create.polygon: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
  • create.polygon: New arguments 'xgrid.at', 'ygrid.at', 'grid.col' to allow for grid lines in the background of the main plot
  • create.violin.plot: New arguments 'extra.points', 'extra.points.cex', 'extra.points.col', to allow for points plotted on top of main plot
  • create.violin.plot: New arguments 'fill.colour', 'border.lwd' to allow for control of interior colours and exterior border widths

BoutrosLab.plotting.general 3.2.24 2012-07-25

MINOR UPDATES

  • create.scatterplot.with.error: New arguments 'strip.col', 'strip.cex' to control size and background colour of panel labels
  • create.scatterplot.with.error: New argument 'error.bar.length' to adjust size of error bar whiskers

BoutrosLab.plotting.general 3.2.23 2012-07-25

MINOR UPDATES

  • create.stripplot: Added parameters for groups, layout, padding around graph, key and legend, and example for how to use 'groups' parameter

BoutrosLab.plotting.general 3.2.22 2012-07-23

MINOR UPDATES

  • default.colours: Changed greyscale warning message for survival palette

BoutrosLab.plotting.general 3.2.21 2012-07-23

MINOR UPDATES

  • create.barplot: Added example using covariates with labels/covariate legend
  • create.scatterplot: Added example using covariates with labels/covariate legend

BoutrosLab.plotting.general 3.2.20 2012-07-22

MINOR UPDATES

  • create.heatmap: Resolved codoc mismatch introduced in v3.2.19
  • Updated package dependencies to newer versions

BoutrosLab.plotting.general 3.2.19 2012-07-20

MINOR UPDATES

  • create.heatmap: Replaced arguments 'border' and 'border.lwd' with 'grid.colour' and 'grid.lwd'
  • create.heatmap: Added ability to turn off interior gridlines using 'grid.row=FALSE', 'grid.col=FALSE' or 'grid.lwd=0'

BoutrosLab.plotting.general 3.2.18 2012-07-17

MINOR UPDATES

  • create.dendrogram: Updated to use jaccard.distance instead of vegdist
  • Removed vegan dependency from DESCRIPTION

BoutrosLab.plotting.general 3.2.17 2012-07-17

MINOR UPDATES

  • panel.BL.bwplot: Changed 'nr' to 'nrow' in matrix call to avoid check warnings
  • default.colours: Changed colours in survival palette

BoutrosLab.plotting.general 3.2.16 2012-07-17

MINOR UPDATES

  • get.corr.key: Added robust regression coefficients and example using outlier
  • Added dependency on package MASS

BoutrosLab.plotting.general 3.2.15 2012-07-16

MINOR UPDATES

  • Changing vegan dependency version to be lower
  • default.colours: Added survival palette and explanation in file as to how to add a new palette

BoutrosLab.plotting.general 3.2.14 2012-07-12

MINOR UPDATES

  • default.colours: Code clean-up and added ability to use chromosome colour scheme

BoutrosLab.plotting.general 3.2.13 2012-07-03

MINOR UPDATES

  • get.corr.key: Changed default resolution in create.survival.plot from 2000 to 100
  • create.histogram: Added support for horizontal and vertical abline

BoutrosLab.plotting.general 3.2.12 2012-06-28

MINOR UPDATES

  • default.colours: Fixed return value for Venn diagram palettes to return a list of both fill colours and text colours, as per example in documentation

BoutrosLab.plotting.general 3.2.11 2012-06-27

MINOR UPDATES

  • create.heatmap: Added 'text.col' parameter
  • create.heatmap: Added example of using unicode symbols instead of text - similar to dotmap, but allows clustering

BoutrosLab.plotting.general 3.2.10 2012-06-26

MINOR UPDATES

  • create.heatmap: Correct ordering of text in clustered data

BoutrosLab.plotting.general 3.2.9 2012-06-15

MINOR UPDATES

  • create.scatterplot: Reordered 'legend' and 'layout.width' arguments to fix padding issues
  • create.scatterplot.with.error: Reordered 'legend' and 'layout.width' arguments to fix padding issues

BoutrosLab.plotting.general 3.2.8 2012-06-12

MINOR UPDATES

  • create.stripplot: Added 'jitter' argument to allow for staggering of data along x-axis

BoutrosLab.plotting.general 3.2.7 2012-06-08

MINOR UPDATES

  • create.histogram: Added parameters for padding, spacing, layout, panel
  • create.histogram: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
  • covariates.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
  • create.multiplot: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac
  • legend.grob: Specifying type = "cairo" for all tiff() calls in Rd files - needed for building package on Mac

BoutrosLab.plotting.general 3.2.6 2012-06-05

MINOR UPDATES

  • create.scatterplot: Added option 'abline.v' to draw vertical lines

BoutrosLab.plotting.general 3.2.5 2012-05-31

MINOR UPDATES

  • create.densityplot: Fixed bug when grids are added - now if type=c("g","l"), xyplot.panels do not double call "g" circle symbols instead of lines
  • create.multiple.boxplots: Updated x-axis label/rotation variable names to match other plotting functions & added argument to allow for specification of main.cex
  • create.stripplot: Updated x-axis rotation variable name to match other plotting functions & added arguments to specify x/ylab.col, x/yaxis.col/tck/rot
  • create.violinplot: Updated x-axis label/rotation variable names to match other plotting functions & added arguments to allow for specification of x/ylab.col, x/yaxis.col/tck/rot

BoutrosLab.plotting.general 3.2.4 2012-05-29

MINOR UPDATES

  • create.histogram: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
  • create.polygon: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col, x/yaxis.rot
  • create.qqplot.comparison: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
  • create.qqplot.fit: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
  • create.scatterplot: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col
  • create.scatterplot.with.error: Added arguments to allow for specification of x/yaxis.col/tck, x/ylab.col

BoutrosLab.plotting.general 3.2.3 2012-05-28

MINOR UPDATES

  • create.barplot: Added example with covariates

BoutrosLab.plotting.general 3.2.2 2012-05-28

MINOR UPDATES

  • create.multiplot: Adjusted formatting and removed debugging code
  • create.scatterplot: Added option 'abline.v' to draw vertical lines
  • create.heatmap: Updated x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'main.cex
  • create.hexbinplot: Updated x/y label variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col', 'xaxis.tck', 'yaxis.tck'
  • create.dotmap: Updated x/y label and x/y cex variable names to match other plotting functions, and added arguments to allow for specification of 'yaxis.rot', 'xaxis.col', 'yaxis.col', 'xlab.col', 'ylab.col'

BoutrosLab.plotting.general 3.2.1 2012-05-18

MINOR UPDATES

  • create.multiplot: Clarified labels on 6 panel example
  • create.barplot: Updated examples to use new variables
  • create.densityplot: Updated examples to include new variables

BoutrosLab.plotting.general 3.2.0 2012-05-16

MAJOR UPDATES

  • create.multiplot: Added example with 6 panels & modified variable names to be consistent
  • create.barplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
  • create.barplot.with.error: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
  • create.boxplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks
  • create.densityplot: Changed x/yaxis label variable names, updated to accept arguments for x/yaxis rotation, x/y axis label and tick label colour, and length of x/y axis tick marks

BoutrosLab.plotting.general 3.1.16 2012-05-15

MINOR UPDATES

  • create.stripplot: Implemented customizable character colour
  • create.multiple.stripplots: Implemented customizable character colour

BoutrosLab.plotting.general 3.1.15 2012-05-14

MINOR UPDATES

  • create.multiplot: Improved consistency of test output file names and variable names
  • create.densityplot: Changed defaults to not display axis lines
  • create.hexbinplot: Changed defaults to not display axis lines
  • create.scatterplot.with.error: Changed defaults to not display axis lines

BoutrosLab.plotting.general 3.1.14 2012-05-11

MINOR UPDATES

  • create.dotmap: Added 'xaxis.lab.cex' and 'yaxis.lab.cex' parameters to specify size of axis labels
  • create.dotmap: Added 'key.top' parameter to specify size of space between colourkey and xaxis.label

BoutrosLab.plotting.general 3.1.13 2012-05-01

MINOR UPDATES

  • create.heatmap: Added 'axes.lwd' parameter to change border width

BoutrosLab.plotting.general 3.1.12 2012-04-25

MINOR UPDATES

  • create.multiplot: Added example combining a stripplot and heatmap

BoutrosLab.plotting.general 3.1.11 2012-04-23

MINOR UPDATES

  • create.heatmap: Added 'xat' and 'yat' parameters to specify label locations

BoutrosLab.plotting.general 3.1.10 2012-04-20

MINOR UPDATES

  • create.scatterplot: Added horizontal abline parameter - able to specify line width and type

BoutrosLab.plotting.general 3.1.9 2012-04-19

MINOR UPDATES

  • create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
  • create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
  • create.heatmap: Added example using covariate legend

BoutrosLab.plotting.general 3.1.8 2012-04-18

MINOR UPDATES

  • create.heatmap: Updated parameter for cell text font size & clarified definitions of 'row.lines' and 'col.lines'

BoutrosLab.plotting.general 3.1.7 2012-04-13

MINOR UPDATES

  • create.heatmap: Added parameters to control text in cells and to manually specify row/column grid vectors
  • legend.grob: Added parameter to specify border colour of legends

BoutrosLab.plotting.general 3.1.6 2012-04-12

MINOR UPDATES

  • create.multiplot: Improved legend functionality
  • create.heatmap: Added ability to insert text in cells & added example

BoutrosLab.plotting.general 3.1.5 2012-04-08

MINOR UPDATES

  • create.heatmap: Added parameters 'title.just' and 'title.fontface' to customize legend titles

BoutrosLab.plotting.general 3.1.5 2012-04-03

MINOR UPDATES

  • create.heatmap: Edited documentation to finalize examples

BoutrosLab.plotting.general 3.1.4 2012-04-02

MINOR UPDATES

  • create.multiplot: Added parameters for more customization - 'main.cex', 'xlab.cex', 'ylab.cex', 'xlimits', 'ylimits'

BoutrosLab.plotting.general 3.1.3 2012-04-19

MINOR UPDATES

  • create.dendrogram: Added 'jaccard' option for calculating distance (for clustering discrete variables)
  • create.heatmap: Added 'jaccard' option for calculating distance (for clustering discrete variables)
  • create.heatmap: Added example using covariate legend

BoutrosLab.plotting.general 3.1.2 2012-03-30

MINOR UPDATES

  • create.heatmap: Updated examples to be fewer and follow a logical progression
  • covariates.grob: Updated examples to be generated using grid.draw() and produce .tiff output
  • legend.grob: Prevented premature closure of user images by removing "dev.off()" call & updated examples to .tiff files using grid.draw()

BoutrosLab.plotting.general 3.1.1 2012-03-21

MINOR UPDATES

  • create.hexbinplot: Altered layout.widths to automatically adjust key.right if colourkey is added (previously right.padding was adjusted and legend was occasionally cut off)

BoutrosLab.plotting.general 3.1.0 2012-03-16

MAJOR UPDATES

  • create.heatmap: Added ability to take more than three colours

BoutrosLab.plotting.general 3.0.9 2012-03-15

MINOR UPDATES

  • create.heatmap: Added parameters 'shrink', 'border', 'border.lwd'
  • create.multiplot: Updated example to use create.heatmap instead of base lattice::levelplot

BoutrosLab.plotting.general 3.0.8 2012-03-09

MINOR UPDATES

  • create.heatmap: Added parameter 'force.clustering' to allow user to ignore the row-limitation
  • create.dendrogram: Added parameter 'force.clustering' to allow user to ignore the row-limitation
  • Updated dependency versions

BoutrosLab.plotting.general 3.0.7 2012-03-09

MINOR UPDATES

  • create.histogram: Removed check of 'x' to ensure it is a formula - problematic is function is called within another function

BoutrosLab.plotting.general 3.0.6 2012-02-21

MINOR UPDATES

  • create.multiplot: Changing default of 'xaxis.alternating' parameter
  • Modified "see also" documentation of plotting functions to include web versions of lattice graphics

BoutrosLab.plotting.general 3.0.5 2012-02-15

MINOR UPDATES

  • Added "see also" sections of documentation of plotting functions for easy referencing

BoutrosLab.plotting.general 3.0.4 2012-02-10

MINOR UPDATES

  • create.multiplot: Added 'panel.widths' parameter & an example to the documentation
  • create.multiplot: Removed internal axes labels in cases where plot axes are identical
  • create.scatterplot: Fixed file formatting to use tabs

BoutrosLab.plotting.general 3.0.3 2012-02-07

MINOR UPDATES

  • create.multiplot: Fixed file formatting to use tabs instead of spaces

BoutrosLab.plotting.general 3.0.2 2012-02-02

MINOR UPDATES

  • create.multiplot: Changed name of example output
  • create.heatmap: Changed default colour scheme to use two colours if data is one-sided and three colours if data is two-sided

BoutrosLab.plotting.general 3.0.1 2012-01-25

MINOR UPDATES

  • create.heatmap: updated documentation to link to related man pages
  • legend.grob: updated documentation to explain implementation decisions

BoutrosLab.plotting.general 3.0.0 2012-01-23

MAJOR UPDATES

  • create.heatmap: Added parameters 'covariate.legends', 'legend.cex', 'legend.title.cex', and 'legend.side' to allow users to include a legend for the covariates
  • legend.grob: Added this function to draw legends

MINOR UPDATES

  • Updated NAMESPACE to rename create.plot.with.levelplot to create.multiplot

BoutrosLab.plotting.general 2.13.1 2012-01-16

MINOR UPDATES

  • create.histogram: Added 'x' parameter to take in formulas, leaving 'data' parameter to take in data

BoutrosLab.plotting.general 2.13.0 2012-01-16

MAJOR UPDATES

  • create.multiplot: Renamed this function - previously called 'create.plot.with.levelplot'
  • create.multiplot: Updated to take any number of plots and display them in the specified layout
  • create.multiplot: Replaced parameters 'plot.object' and 'levelplot.object' with 'plot.objects
  • create.multiplot: Replaced parameter 'spacing' with 'yspacing'
  • create.multiplot: Added parameters 'xspacing' and 'plot.layout'

BoutrosLab.plotting.general 2.12.5 2012-01-11

MINOR UPDATES

  • create.barplot: Added parameter 'border.col' to control border colour

BoutrosLab.plotting.general 2.12.4 2012-01-11

MINOR UPDATES

  • create.barplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line

BoutrosLab.plotting.general 2.12.3 2012-01-11

MINOR UPDATES

  • create.boxplot: Added parameters 'abline.h', 'abline.type', 'abline.lwd', 'abline.col' to add superimposed line

BoutrosLab.plotting.general 2.12.2 2012-01-10

MINOR UPDATES

  • create.barplot: Added 'panel.abline'
  • create.boxplot: Added 'panel.abline'
  • create.heatmap: Added parameters 'xlab', 'ylab' and ability to place x-axis label on top axis
  • create.plot.with.levelplot: Added error checking for trellis objects

BoutrosLab.plotting.general 2.12.1 2012-01-10

MINOR UPDATES

  • create.heatmap: Added ability to plot covariates without dendrograms
  • create.heatmap: Added parameters 'row.dendrogram' and 'col.dendrogram' to allow users to pass in dendrograms
  • Added two functions - create.dendrogram() and covariates.grob()

BoutrosLab.plotting.general 2.12.0 2012-01-10

MINOR UPDATES

  • get.defaults: Set unix to fall back on default fonts

BoutrosLab.plotting.general 2.11.10 2012-01-06

MINOR UPDATES

  • create.plot.with.levelplot: Updated border example

BoutrosLab.plotting.general 2.11.9 2012-01-04

  • Committing new version

BoutrosLab.plotting.general 2.11.8 2012-01-04

MINOR UPDATES

  • create.plot.with.levelplot: Improved ability to control axis labels
  • create.plot.with.levelplot: Added padding parameters

BoutrosLab.plotting.general 2.11.7 2011-12-23

MINOR UPDATES

  • Minor change to DESCRIPTION

BoutrosLab.plotting.general 2.11.6 2011-12-22

MINOR UPDATES

  • create.scatterplot: Updated to allow for parameters of length one specify properties of all curves with 'add.curves' option
  • create.scatterplot: Added warning for cases when curves are drawn with data containing groups where grouping variables are being removed

BoutrosLab.plotting.general 2.11.5 2011-12-16

MINOR UPDATES

  • create.plot.with.levelplot: Reformatted example code

BoutrosLab.plotting.general 2.11.4 2011-12-15

MINOR UPDATES

  • create.plot.with.levelplot: Improved readability of parameter list
  • create.scatterplot: Updated panel.curve code to avoid 'no visible binding for global variable x' error

BoutrosLab.plotting.general 2.11.3 2011-12-13

MINOR UPDATES

  • create.scatterplot.with.error: Minor formatting fix to example
  • create.scatterplot: Added parameter 'key.top' to control spacing above the key

BoutrosLab.plotting.general 2.11.2 2011-12-13

MINOR UPDATES

  • create.heatmap: Renamed parameter 'data.to.cluster' with 'x'

BoutrosLab.plotting.general 2.11.1 2011-12-13

MINOR UPDATES

  • create.heatmap: Cleaned up code by removing spurious print statements

BoutrosLab.plotting.general 2.11.0 2011-12-13

MAJOR UPDATES

  • Updated many plotting examples have better clarity and use default.colours()

MINOR UPDATES

  • default.colours: Standardized error-handling
  • create.dotmap: Changed default colour scheme

BoutrosLab.plotting.general 2.10.12 2011-12-13

MINOR UPDATES

  • create.heatmap: Renamed parameters 'names.row' and 'names.col' with 'xaxis.lab' and 'yaxis.lab'
  • create.heatmap: Added new parameter 'xaxis.col' to set colours of axis labels

BoutrosLab.plotting.general 2.10.11 2011-12-13

MINOR UPDATES

  • create.heatmap: Cleaned up code by standardizing variable names and adjusting error-handling

BoutrosLab.plotting.general 2.10.10 2011-12-12

MINOR UPDATES

  • optimal.heatmap.cex.txt: Improved formatting of header
  • create.heatmap: Cleaned up code
  • create.heatmap: Added example of how to specify row and column labels

BoutrosLab.plotting.general 2.10.9 2011-12-12

MINOR UPDATES

  • create.scatterplot: Changed formatting to produce a smaller gap between title and plot
  • create.scatterplot: Updated example to include legend and filename

BoutrosLab.plotting.general 2.10.8 2011-12-06

MINOR UPDATES

  • create.scatterplot: Cleaned up code by removing inverted line
  • Updated default value of 'strip.col' to 'white' instead of 'grey'

BoutrosLab.plotting.general 2.10.7 2011-12-02

MINOR UPDATES

  • create.scatterplot: Added example to draw colour depth to scatterpoints

BoutrosLab.plotting.general 2.10.6 2011-12-01

BUG FIXES

  • create.scatterplot: Fixed bug in default behaviour for 'curve.from' and 'curve.to' parameters

MINOR UPDATES

  • create.scatterplot: Updated example

BoutrosLab.plotting.general 2.10.5 2011-12-01

MINOR UPDATES

  • create.scatterplot: Cleaned up code

BoutrosLab.plotting.general 2.10.4 2011-11-30

MINOR UPDATES

  • create.scatterplot: Replace parameter 'add.lines' with 'add.curves', this allowing the user to draw any segment of any curve that can be specified with a function
  • create.scatterplot: Added example to demonstrate use of 'add.curves' parameter
  • create.polygon: Fixed 'alternating' parameter to force x-axis labels to be on the bottom row
  • create.polygon: Updated example

BoutrosLab.plotting.general 2.10.3 2011-11-29

MINOR UPDATES

  • create.polygon: Updated 'top.padding' and 'bottom.padding' parameters
  • create.scatterplot: Added ability to draw line segments on plotting region

BoutrosLab.plotting.general 2.10.2 2011-11-17

MINOR UPDATES

  • create.violin.plot: Updated to allow boundaries and scaling

BoutrosLab.plotting.general 2.10.1 2011-11-17

MINOR UPDATES

  • create.plot.with.levelplot: Added this function by merging 'create.boxplot.with.levelplot' and 'create.scatterplot.with.levelplot'

BoutrosLab.plotting.general 2.10.0 2011-10-27

MAJOR UPDATES

  • create.scatterplot.with.levelplot: Added this function

BoutrosLab.plotting.general 2.9.44 2011-10-24

MINOR UPDATES

  • Temporary change to lattice dependency version

BoutrosLab.plotting.general 2.9.43 2011-10-12

MINOR UPDATES

  • create.heatmap: Added parameters to support ?dist based distance measures for clustering
  • create.hexbinplot: Added warning if specified 'maxcnt' is less than the actual max count

BoutrosLab.plotting.general 2.9.42 2011-09-28

MINOR UPDATES

  • create.boxplot: Updated to force axis labels to always be on the left or bottom

BoutrosLab.plotting.general 2.9.41 2011-09-27

MINOR UPDATES

  • Added 'as.table' parameter to plotting functions to allow for panel ordering

BoutrosLab.plotting.general 2.9.40 2011-09-21

MINOR UPDATES

  • create.qqplot.comparison: Added option of choosing difference methods to draw a reference line
  • create.qqplot.fit: Added option of choosing difference methods to draw a reference line
  • create.qqplot.fit: Added ability to draw confidence bands for grouped data

BoutrosLab.plotting.general 2.9.39 2011-09-20

MINOR UPDATES

  • create.dotmap: Standardized parameter names

BoutrosLab.plotting.general 2.9.38 2011-09-14

MINOR UPDATES

  • create.dotmap: Added example of using 'padding.text'

BoutrosLab.plotting.general 2.9.37 2011-09-13

MINOR UPDATES

  • create.qqplot.fit: Added polygon plots for confidence intervals
  • create.scatterplot: Fixed 'add.axes' parameter default value in documentation

BoutrosLab.plotting.general 2.9.36 2011-09-13

MINOR UPDATES

  • create.scatterplot: Changed default value of 'add.axes' parameter to FALSE
  • default.colours: Change output format to be returned, rather than printed
  • create.polygon: Added 'use.loess.median' and 'use.loess.border' parameters

BoutrosLab.plotting.general 2.9.35 2011-09-08

MINOR UPDATES

  • change dependency version for package BoutrosLab.statistics.general

BoutrosLab.plotting.general 2.9.34 2011-09-05

MINOR UPDATES

  • create.barplot: Added parameters to change colour and font size of the panel title
  • create.boxplot: Added parameters to change colour and font size of the panel title
  • create.polygon: Added parameters to change colour and font size of the panel title
  • create.scatterplot: Added parameters to change colour and font size of the panel title

BoutrosLab.plotting.general 2.9.33 2011-09-01

MINOR UPDATES

  • Added 'rgb.to.greyscale' function to NAMESPACE

BoutrosLab.plotting.general 2.9.32 2011-09-01

BUG FIXES

  • create.hexbinplot: Removed appearance of artificial blue dot at origin

BoutrosLab.plotting.general 2.9.31 2011-09-01

MINOR UPDATES

  • rgb.to.greyscale: Added function to BoutrosLab.plotting.general

BoutrosLab.plotting.general 2.9.30 2011-08-30

MINOR UPDATES

  • create.qqplot.fit: Changes to ensure expected functionality

BoutrosLab.plotting.general 2.9.29 2011-08-30

MINOR UPDATES

  • create.qqplot.fit: Deleted function 'single.qqplot.CI' and revised corresponding part in function 'create.qqplot.fit'

BoutrosLab.plotting.general 2.9.28 2011-08-30

MINOR UPDATES

  • Updated maintainer email
  • Removed dependency on package 'distr'

BoutrosLab.plotting.general 2.9.27 2011-08-26

MINOR UPDATES

  • create.histogram: Changed formatting of documentation
  • create.multiple.stripplots: Added 'ylab.axis.padding' parameter

BoutrosLab.plotting.general 2.9.26 2011-08-26

MINOR UPDATES

  • default.colours: Added new function to provide colour schemes for plotting

BoutrosLab.plotting.general 2.9.25 2011-08-25

MINOR UPDATES

  • optimal.heatmap.cex.txt: Added lookup file for setting default font sizes for heatmaps of varying size
  • create.heatmap: Changed to set default font sizes from lookup file (based on size of input)

BoutrosLab.plotting.general 2.9.24 2011-08-24

MINOR UPDATES

  • create.polygon: Cleaned up code

BoutrosLab.plotting.general 2.9.23 2011-08-24

MINOR UPDATES

  • create.multiple.boxplots: Added 'ylab.axis.padding' and 'ylab.cex' parameters

BoutrosLab.plotting.general 2.9.22 2011-08-24

MINOR UPDATES

  • create.dotmap: Changed default grid line colour to grey when no background colour is present

BoutrosLab.plotting.general 2.9.21 2011-08-23

MINOR UPDATES

  • single.qqplot.CI: Removed 'subset' function

BoutrosLab.plotting.general 2.9.20 2011-08-23

MINOR UPDATES

  • create.qqplot.comparison: Fixed examples

BoutrosLab.plotting.general 2.9.19 2011-08-23

MINOR UPDATES

  • create.qqplot.comparison: Fixed examples

BoutrosLab.plotting.general 2.9.18 2011-08-23

MINOR UPDATES

  • create.qqplot.comparison: Added functionality of drawing confidence bands
  • create.qqplot.comparison: Changed label default behaviour
  • create.qqplot.fit: Changed label default behaviour
  • create.dotmap: Changed default grid line colour to black if background colour is present
  • create.polygon: Fixed grouping functionality and example
  • create.polygon: Added translucent colours

BoutrosLab.plotting.general 2.9.17 2011-08-16

MINOR UPDATES

  • create.polygon: Changed input parameter settings to be more intuitive
  • create.polygon: Added examples (including grouping example)

BoutrosLab.plotting.general 2.9.16 2011-08-16

MINOR UPDATES

  • create.scatterplot: Removed redundancy in code by parameterizing y=x line, and changed example

BoutrosLab.plotting.general 2.9.15 2011-08-15

MINOR UPDATES

  • create.boxplot.with.levelplot: Added more examples

BoutrosLab.plotting.general 2.9.14 2011-08-13

MINOR UPDATES

  • create.qqplot.fit: Improvements to code formatting
  • create.qqplot.comparison: Improvements to code formatting
  • single.qqplot.CI: Improvements to code formatting

BoutrosLab.plotting.general 2.9.13 2011-08-11

MINOR UPDATES

  • create.hexbinplot: Added 'xaxis.labels' and 'yaxis.labels' parameters
  • create.boxplot.with.levelplot: Improved example

BoutrosLab.plotting.general 2.9.12 2011-08-11

MINOR UPDATES

  • create.barplot: Added panel parameters
  • create.scatterplot: Added panel parameters and improved input method of 'groups' parameter
  • boxplot.with.levelplot: Cleaned up example names
  • create.polygon: Cleaned up example names

BoutrosLab.plotting.general 2.9.11 2011-08-10

MINOR UPDATES

  • create.scatterplot: Added 'layout' and 'xaxis.tck' parameters to specify figure arrangement and length of tick marks
  • create.scatterplot: Added example to show lines connecting dots to the x-axis
  • get.corr.key: Added 'key.cex' parameter to allow users to specify font size of the key

BoutrosLab.plotting.general 2.9.10 2011-08-08

MINOR UPDATES

  • create.qqplot.fit: Added example
  • single.qqplot.CI: Renamed from 'qq.single.CI' and updated examples and documentation

BoutrosLab.plotting.general 2.9.9 2011-08-08

MINOR UPDATES

  • qq.single.CI: Renamed from 'envelop' function
  • create.qqplot.comparison: Renamed from 'create.qqplot2' function
  • create.qqplot.fit: Renamed from 'create.qqplot' function
  • create.scatterplot: Updated example output names for consistency

BoutrosLab.plotting.general 2.9.8 2011-08-06

MINOR UPDATES

  • create.qqplot: Code-review
  • create.qqplot2: Code-review

BoutrosLab.plotting.general 2.9.7 2011-08-05

MINOR UPDATES

  • envelope: Added function to create one-sample qqplot
  • create.qqplot: Updated code and documentation
  • create.qqplot2: Updated code and documentation

BoutrosLab.plotting.general 2.9.6 2011-08-05

MINOR UPDATES

  • create.qqplot2: Added function to create two-sample qq plots
  • create.qqplot: Added function to create one-sample qq plots
  • create.boxplot.with.levelplot: Updated documentation
  • create.polygon: Updated documentation

BoutrosLab.plotting.general 2.9.5 2011-08-03

MINOR UPDATES

  • create.heatmap: Added 'print.color.key' parameter to enable turning "off" of colourkey printing

BoutrosLab.plotting.general 2.9.4 2011-08-03

MINOR UPDATES

  • create.boxplot.with.levelplot: Added new function
  • create.polygon: Added new function

BoutrosLab.plotting.general 2.9.3 2011-08-02

MINOR UPDATES

  • create.violin.plot: Updated examples
  • Updated package dependencies

BoutrosLab.plotting.general 2.9.2 2011-07-25

MINOR UPDATES

  • create.dotmap: Updated documentation
  • Updated package dependencies

BoutrosLab.plotting.general 2.9.1 2011-07-23

MINOR UPDATES

  • create.boxplot: Added 'x.tck' parameter to control length of tick marks

BoutrosLab.plotting.general 2.9.0 2011-07-21

MINOR UPDATES

  • create.dotmap: Added new plotting function

BoutrosLab.plotting.general 2.8.3 2011-07-14

MINOR UPDATES

  • create.boxplot: Added panel parameters
  • create.heatmap: Added 'x.alternating' parameter to control position of x-axis labels
  • Added warning to documentation of plotting functions to alert users of ineffective methods of running functions

BoutrosLab.plotting.general 2.8.2 2011-06-27

MINOR UPDATES

  • create.multiple.stripplots: Added 'type' parameter to allow users to change the type of plotting characters
  • create.heatmap: Added 'xlab' and 'ylab' parameters

BoutrosLab.plotting.general 2.8.1 2011-06-22

MINOR UPDATES

  • create.heatmap: Added functionality of removing column and/or row grid-lines
  • Updated package dependency versions

BoutrosLab.plotting.general 2.8.0 2011-06-17

MAJOR UPDATES

  • create.multiple.stripplots: Added new plotting function to create multiple stripplots

MINOR UPDATES:

  • create.multiple.boxplots: Added 'header.cex' parameter to control font size of the header

BoutrosLab.plotting.general 2.7.7 2011-06-16

MINOR UPDATES

  • create.violin.plot: Added 'xaxis.labels' and 'yaxis.labels' parameters to control axes labelling
  • create.heatmap: Added 'top.padding' and 'bottom.padding' parameters to control top and bottom margins

BoutrosLab.plotting.general 2.7.6 2011-06-08

MINOR UPDATES

  • Updated plotting functions for NAMESPACE

BoutrosLab.plotting.general 2.7.5 2011-06-08

MINOR UPDATES

  • create.histogram: Added 'lwd' and 'lty' parameters to control line width and line style
  • create.histogram: Fixed code to work without axes labels
  • create.scatterplot: Added 'lty' parameter to control line style and adjusted example
  • create.scatterplot.with.error: Added 'lty' parameter and adjusted example

BoutrosLab.plotting.general 2.7.4 2011-06-07

MINOR UPDATES

  • Added NAMESPACE

BoutrosLab.plotting.general 2.7.3 2011-05-31

MINOR UPDATES

  • get.corr.key: Fixed syntax error in example
  • create.boxplot: Reverted functionality to use panel.BL.bwplot
  • create.scatterplot: Updated examples
  • create.histogram: Updated examples
  • create.scatterplot.with.error: Updated examples
  • create.violinplot: Updated examples

BoutrosLab.plotting.general 2.7.2 2011-05-19

MINOR UPDATES

  • create.heatmap: Added 'right.padding' and 'left.padding' parameters to control margins

BoutrosLab.plotting.general 2.7.1 2011-05-17

MINOR UPDATES

  • get.corr.key: Cleaned code
  • create.hexbinplot: Cleaned code and fixed links in documentation

BoutrosLab.plotting.general 2.7.0 2011-05-12

BUG FIXES

  • create.hexbinplot: Changed implementation to address critical issues related to 'maxcnt' argument

MINOR UPDATES:

  • create.hexbinplot: Updated documentation with links and example
  • create.barplot: Updated example
  • create.densityplot: Updated example

BoutrosLab.plotting.general 2.6.7 2011-05-11

MINOR UPDATES

  • get.corr.key: Added 'alpha.background' parameter
  • create.hexbinplot: Development version - bug related to 'maxcnt' parameter

BoutrosLab.plotting.general 2.6.6 2011-05-02

MINOR UPDATES

  • get.corr.key: Fixed error
  • create.hexbinplot: Added 'grid' and 'abline' parameters and corresponding example

BoutrosLab.plotting.general 2.6.5 2011-05-02

MINOR UPDATES

  • create.hexbinplot: Added 'colorcut', 'mincnt', 'maxcnt' parameters to allow user to specify number of bins in plot

BoutrosLab.plotting.general 2.6.4 2011-04-28

MINOR UPDATES

  • get.corr.key: Improved code formatting
  • get.corr.key: Added 'beta0' and 'beta1' options to the key
  • create.hexbinplot: Added 'aspect' parameter to adjust plot size

BoutrosLab.plotting.general 2.6.3 2011-04-21

MINOR UPDATES

  • create.hexbinplot: Added 'xaxis.cex' and 'yaxis.cex' parameters

BoutrosLab.plotting.general 2.6.2 2011-04-04

MINOR UPDATES

  • create.boxplot: Updated code to remove unnecessary dependencies
  • create.boxplot: Added 'fill' parameter to control the fill colour and corresponding example
  • create.scatterplot: Updates to the examples

BoutrosLab.plotting.general 2.6.1 2011-04-01

MINOR UPDATES

  • create.dotmap: Reintroduced 'key' parameter into function
  • create.dotmap: Added 'legend' parameter to allow for multiple keys

BoutrosLab.plotting.general 2.6.0 2011-03-13

MAJOR UPDATES

  • create.scatterplot: Updated functionality to allow for log-scale x- and y-axes

MINOR UPDATES

  • create.scatterplot: Cleaned up documentation

BoutrosLab.plotting.general 2.5.7 2011-03-11

MINOR UPDATES

  • create.densityplot: Added 'xaxis.labels' and 'yaxis.labels' parameters

BoutrosLab.plotting.general 2.5.6 2011-03-10

MINOR UPDATES

  • create.violin.plot: Added example using legend

BoutrosLab.plotting.general 2.5.5 2011-03-10

MINOR UPDATES

  • create.scatterplot.with.error: Added example using legend
  • create.scatterplot: Updated example

BoutrosLab.plotting.general 2.5.4 2011-03-10

MINOR UPDATES

  • create.hexbinplot: Added example using legend
  • create.histogram: Added example using legend

BoutrosLab.plotting.general 2.5.3 2011-03-10

MINOR UPDATES

  • create.boxplot: Added example using legend
  • create.densityplot: Added example using legend

BoutrosLab.plotting.general 2.5.2 2011-03-10

MINOR UPDATES

  • create.barplot.with.error: Added example using legend

BoutrosLab.plotting.general 2.5.1 2011-03-10

MINOR UPDATES

  • create.barplot: Added example using legend

BoutrosLab.plotting.general 2.5.0 2011-03-09

MINOR UPDATES

  • create.barplot.with.error: Updated example

BoutrosLab.plotting.general 2.4.0 2011-03-08

MINOR UPDATES

  • create.dotmap: Removed 'legend' parameter
  • create.scatterplot: Updated example filenames
  • create.scatterplot: Added example using legend
  • create.barplot.with.error: Cleaned up code
  • create.densityplot: Updated code to use a single panel function

BoutrosLab.plotting.general 2.3.3 2011-03-03

MINOR UPDATES

  • create.heatmap: Updated examples to be sequential and added example using covariates

BoutrosLab.plotting.general 2.3.2 2011-02-23

MINOR UPDATES

  • create.scatterplot: Added 'abline' argument
  • create.scatterplot.with.error: Added 'abline' argument

BoutrosLab.plotting.general 2.3.1 2011-02-23

MINOR UPDATES

  • create.scatterplot: Added ability to add multiple keys to a single plot

BoutrosLab.plotting.general 2.3.0 2011-02-22

MINOR UPDATES

  • create.scatterplot: Cleaned up code to use a single panel function
  • create.scatterplot.with.error: Cleaned up code to use a single panel function
  • create.scatterplot.with.error: Updated formatting to use tabs instead of spaces
  • create.scatterplot.with.error: Cleaned up documentation and examples

BUG FIXES

  • create.scatterplot.with.error: Fixed bug that prevented keys from being plotted

BoutrosLab.plotting.general 2.2.0 2011-02-22

MINOR UPDATES

  • create.densityplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
  • create.scatterplot: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example
  • create.scatterplot.with.error: Changed 'xat' and 'yat' parameters into 'xgrid.at' and 'ygrid.at' parameters to specify grid lines and added example

BoutrosLab.plotting.general 2.1.0 2011-02-22

MAJOR UPDATES

  • Added 'legend' and 'key' parameters to plotting functions

MINOR UPDATES

  • create.scatterplot: Added example using a legend

BoutrosLab.plotting.general 2.0.24 2011-02-21

BUG FIXES

  • get.corr.key: Fixed bug related to using phantom instead of phantom(0)

BoutrosLab.plotting.general 2.0.23 2011-02-19

MINOR UPDATES

  • create.barplot: Updated to allow use of non-factorial variables for grouping

BoutrosLab.plotting.general 2.0.22 2011-02-17

BUG FIXES

  • create.scatterplot.with.error: Fixed error related to grid

BoutrosLab.plotting.general 2.0.21 2011-02-14

BUG FIXES

  • create.scatterplot: Fixed error related to 'ylimits' and 'xlimits', 'yat' and 'xat
  • create.scatterplot.with.error: Fixed error related to grouped line graphs

BoutrosLab.plotting.general 2.0.20 2011-02-13

MINOR UPDATES

  • create.barplot: Changed to prevent spurious warnings when specifying colours with ungrouped data

BoutrosLab.plotting.general 2.0.19 2011-02-11

MINOR UPDATES

  • create.heatmap: Updated examples

BoutrosLab.plotting.general 2.0.18 2011-02-11

MINOR UPDATES

  • create.heatmap: Cleaned up code to remove deprecated parameter 'colour.number.tweak'

BoutrosLab.plotting.general 2.0.17 2011-02-09

MINOR UPDATES

  • create.scatterplot: Cleaned up examples to all use the same dataset

BoutrosLab.plotting.general 2.0.16 2011-02-07

MINOR UPDATES

  • create.scatterplot.with.error: Cleaned up code to match documentation

BoutrosLab.plotting.general 2.0.15 2011-02-04

MINOR UPDATES

  • generate.at.final: Added function to add tick marks to plots

BoutrosLab.plotting.general 2.0.14 2011-01-31

MINOR UPDATES

  • get.corr.key: Added documentation to function for automatically generating a legend with correlation, beta, and p-values

BoutrosLab.plotting.general 2.0.13 2011-01-31

MINOR UPDATES

  • get.corr.key: Updated to code
  • Updated required packages

BoutrosLab.plotting.general 2.0.12 2011-01-25

MINOR UPDATES

  • generate.at.final: Added documentation
  • get.corr.key: Added option of including beta

BUG FIXES

  • create.densityplot: Addressed problem of grid drawing and tick mark locations not lining up when both are required - this achieved by removing default grid lines and redrawing them using panel.abline() at user-specified locations

BoutrosLab.plotting.general 2.0.11 2011-01-17

MINOR UPDATES

  • get.corr.key: Added flexibility to have rho in Greek
  • write.plot: Added functionality to call CairoTIFF if default tiff has problems
  • create.dotmap: Updated default value of 'xaxis.lab' and 'yaxis.lab' to NULL in order to accept expressions

BoutrosLab.plotting.general 2.0.10 2011-01-07

MINOR UPDATES

  • get.corr.key: Added function to add basic correlation key to scatter-like plots
  • create.barplot: Updated documentation and examples to use more complex datasets and demonstrate use of 'ylim' and 'yat' parameters
  • create.barplot: Added 'key' parameter
  • create.barplot: Changed 'groups' parameter to accept an expression or variable

BoutrosLab.plotting.general 2.0.9 2010-12-22

MINOR UPDATES

  • create.barplot: Added filename to stacked barplot examples

BUG FIXES

  • create.barplot: Fixed problem with groups
  • create.barplot.with.error: Fixed problem with groups

BoutrosLab.plotting.general 2.0.8 2010-12-21

MINOR UPDATES

  • create.barplot: Added user-control for colour picking for groups
  • create.barplot.with.error: Added user-control for colour picking for groups
  • create.barplot: Added 'group' and 'stack' parameters

BoutrosLab.plotting.general 2.0.7 2010-11-29

MINOR UPDATES

  • create.scatterplot: Added ability to rotate text in axis labels

BoutrosLab.plotting.general 2.0.6 2010-11-17

MINOR UPDATES

  • create.scatterplot.with.error: Added group-specific error bar colour handling under no conditioning

BoutrosLab.plotting.general 2.0.5 2010-11-17

MINOR UPDATES

  • create.scatterplot.with.error: Added 'add.axes' parameter

BoutrosLab.plotting.general 2.0.4 2010-11-16

MINOR UPDATES

  • create.scatterplot.with.error: Added ability to handle grouped data

BoutrosLab.plotting.general 2.0.3 2010-11-15

MINOR UPDATES

  • create.scatterplot: Added 'xaxis.labels' and 'yaxis.labels' parameter to allow customization of axis labels
  • get.defaults: Updated to handle font changes with R v2.12.0
  • create.dotmap: Updated examples

BoutrosLab.plotting.general 2.0.2 2010-11-15

MINOR UPDATES

  • create.scatterplot: Added ability to handle grouped data

BoutrosLab.plotting.general 2.0.1 2010-11-11

MINOR UPDATES

  • Updated platform-specific code to work better with changes in R v2.12.0

BoutrosLab.plotting.general 2.0.0 2010-11-02

MAJOR UPDATES

  • Updated package dependencies
  • Updated all plotting functions to take a main title
  • get.defaults: Fixed bug related to changes in newest versions of R and lattice
  • create.heatmap: Updated colouring functionality to reduce possibility of error
  • create.histogram: Added functionality of colouring bars
  • create.hexbinplot: Added functionality of specifying label sizes

BoutrosLab.plotting.general 1.11.2 2010-10-26

MINOR UPDATES

  • create.boxplot: Added 'lwd' parameter to support production of smaller images

BoutrosLab.plotting.general 1.11.1 2010-10-20

MINOR UPDATES

  • create.boxplot: Updated to facilitate horizontal boxplots annotations for x-axis

BoutrosLab.plotting.general 1.11.0 2010-10-14

MAJOR UPDATES

  • write.plot: Added new function to standardize plotting output - now used in all plotting functions

MINOR UPDATES

  • create.barplot.with.error: Changed default line width of bar outline to match line width of error bar
  • create.barplot: Updated layout of figure to match other plotting functions
  • Removed 'compression' parameter from plotting functions

BoutrosLab.plotting.general 1.10.1 2010-09-23

MINOR UPDATES

  • create.multiple.boxplots: Reordered parameters to be consisting with other plotting functions
  • create.multiple.boxplots: Added 'symbol.cex' parameter to control size of boxplot dots

BoutrosLab.plotting.general 1.10.0 2010-09-22

BUG FIXES

  • create.boxplot: Fixed so that 'ylimits' argument is no longer silently ignored

BoutrosLab.plotting.general 1.9.21 2010-09-16

MINOR UPDATES

  • create.violin.plot: Updated documentation to clarify circumstances when 'x' will be coerced to a factor or shingle (when horizontal argument set to FALSE)
  • create.hexbinplot: Added 'compression' and 'add.axes' parameters

BoutrosLab.plotting.general 1.9.20 2010-09-15

MINOR UPDATES

  • create.multiple.boxplots: Updated 'right.padding' to be set to 2
  • create.barplot.with.error: Renamed function from create.barplot.with.error.r into create.barplot.with.error.R

BoutrosLab.plotting.general 1.9.19 2010-09-12

MINOR UPDATES

  • Updated documentation of plotting functions
  • Updated plotting functions to output a trellis object by default

BoutrosLab.plotting.general 1.9.18 2010-09-03

BUG FIXES

  • create.barplot: Fixed bug that prevented implicit grouping from working
  • create.barplot.with.error: Fixed bug that prevented implicit grouping from working
  • create.scatterplot.with.error: Fixed bug that prevented implicit grouping from working

BoutrosLab.plotting.general 1.9.17 2010-08-31

BUG FIXES

  • create.scatterplot: Fixed bug that prevented implicit grouping from working

BoutrosLab.plotting.general 1.9.16 2010-08-27

MINOR UPDATES

  • create.barplot.with.error: Added function to create barplots with customizable error bars

BoutrosLab.plotting.general 1.9.15 2010-08-26

MINOR UPDATES

  • create.violinplot: Added 'horizontal' parameter to allow user to specify whether to plot horizontally or vertically
  • create.scatterplot.with.error: Added 'y.error.up', 'y.error.down', 'x.error.right', 'x.error.left' parameter to allow for drawing horizontal and/or vertical error bars (removed 'error.plus' and 'error.minus' parameters)
  • create.scatterplot.with.error: Added 'x.error.bar.col' and 'y.error.bar.col' parameters
  • create.scatterplot.with.error: Added 'error.whisker.angle' parameter to control the angle of whiskers drawn at both ends of the error bars

BoutrosLab.plotting.general 1.9.14 2010-08-19

MINOR UPDATES

  • create.boxplot: Added 'xaxis.labels' parameter

BoutrosLab.plotting.general 1.9.13 2010-08-15

MINOR UPDATES

  • Added warnings framework to plotting functions
  • Updated functions to correctly deal with postscript graphics device
  • Reimplemented fonts mechanism to support Win/*Nix systems correctly w.r.t postscript specific exceptions
  • create.heatmap: Added 'cor.method' parameter

BUG FIXES

  • panel.BL.bwplot: Fixed function to show outlier points properly when input argument box.colour is a vector

BoutrosLab.plotting.general 1.9.12 2010-08-07

MINOR UPDATES

  • create.barplot: Updated default to give x-axis and y-axis scale labels

BoutrosLab.plotting.general 1.9.11 2010-08-07

MINOR UPDATES

  • Updated plotting functions to offer OS specific settings framework

BoutrosLab.plotting.general 1.9.10 2010-08-07

MINOR UPDATES

  • Updated plotting function documentation with "See Also" links and standardizations to the "Value" section
  • create.heatmap: Renamed 'legend.cex' parameter to 'colorkey.cex'

BoutrosLab.plotting.general 1.9.9 2010-08-06

MINOR UPDATES

  • Updated plotting functions to have the same default font type

BoutrosLab.plotting.general 1.9.8 2010-08-05

BUG FIXES:

  • create.heatmap: Fixed functionality of 'colour.alpha' parameter

MINOR UPDATES

  • create.heatmap: Added example to demonstrate usage of 'colour.alpha' parameter

BoutrosLab.plotting.general 1.9.7 2010-08-04

MINOR UPDATES

  • create.scatterplot.with.error: Added function to create scatterplot with error bars overlaid

BoutrosLab.plotting.general 1.9.6 2010-08-04

MINOR UPDATES

  • create.barplot: Added 'yaxis.labels' parameter
  • create.scatterplot: Changed panel function to allow for update() to change conditioned trellis object
  • create.multiple.boxplots: Changed c() to stack() to accommodate data.frames
  • create.violin.plot: Updated to match other plotting functions

BoutrosLab.plotting.general 1.9.5 2010-07-29

MINOR UPDATES

  • create.barplot: Added 'col' parameter to control the fill colour of bars
  • create.scatterplot: Added default values for some parameters
  • create.stripplot: Added default values for some parameters
  • create.violinplot: Added default values for some parameters

BoutrosLab.plotting.general 1.9.4 2010-07-26

MINOR UPDATES

  • create.barplot: Renamed parameters to standardize with other plotting functions
  • create.multiple.boxplots: Renamed parameters to standardize with other plotting functions
  • create.heatmap: Added verbose warning when function cannot generate a figure
  • create.boxplot: Fixed broken default handling of y-axis scale labels

BoutrosLab.plotting.general 1.9.3 2010-06-29

BUG FIXES

  • create.heatmap: Fixed bug to accept NAs when specifying colour-ranges

BoutrosLab.plotting.general 1.9.2 2010-06-28

MINOR UPDATES

  • create.barplot: Changed 'xlab' and 'ylab' parameters into 'xlab.label' and 'ylab.label' and reordered parameters
  • create.boxplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', and 'ylabel.cex' parameters into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
  • create.hexbinplot: Changed 'xlabel', 'ylabel' parameters into 'xlab.label', 'ylab.label'
  • create.stripplot: Changed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' into 'xlab.lab', 'ylab.lab', 'xlab.cex', 'ylab.cex' and reordered parameters
  • create.violinplot: Changed 'ylabel' parameter into 'ylab.label'
  • create.histogram: Adjusted example
  • create.multiple.boxplots: Adjusted example

BoutrosLab.plotting.general 1.9.1 2010-06-25

MINOR UPDATES

  • create.scatterplot: Renamed 'xlabel', 'ylabel', 'xlabel.cex', 'ylabel.cex' parameters to 'xlab.label', 'ylab.label', 'xlab.cex', 'ylab.cex'
  • create.histogram: Changed default to plot percentages instead of densities
  • create.scatterplot: Adjusted example to show extra features

BoutrosLab.plotting.general 1.9.0 2010-06-24

MAJOR UPDATES

  • create.densityplot: Added new function to plot densities

MINOR UPDATES

  • create.histogram: Added many new parameters, changed order of parameters, renamed parameters for standardization
  • create.boxplot: Improved example
  • create.histogram: Improved example

BoutrosLab.plotting.general 1.8.1 2010-06-24

MINOR UPDATES

  • Updated parameter ordering of plotting functions to bring 'filename' parameter to the front of each function, and the height, width, and resolution parameters to the back

BoutrosLab.plotting.general 1.8.0 2010-06-24

MAJOR UPDATES

  • Updated plotting functions to return the trellis object only if filename = NULL
  • All example files are named after the method that produced them
  • Standardized variable names of plotting objects to trellis.object

MINOR UPDATES

  • create.multiple.boxplots: Fixed spacing/indentation to match coding standard
  • create.histogram: Reordered parameters to have mandatory parameters come first
  • create.stripplot: Reordered parameters to have mandatory parameters come first
  • create.violinplot: Reordered parameters to have mandatory parameters come first
  • create.histogram: Allowed lattice default values for breaks, ylimits, etc
  • create.violinplot: Allowed lattice default values for ylimits, yat

BoutrosLab.plotting.general 1.7.3 2010-06-23

MINOR UPDATES

  • create.heatmap: Added examples to documentation

BoutrosLab.plotting.general 1.7.2 2010-06-22

BUG FIXES

  • create.heatmap: Fixed but in example by changing dataset
  • scientific.notation.2: Fixed function to display the last digit as 0 when requested

MINOR UPDATES

  • create.heatmap: Added 'colorkey.labels' parameter

BoutrosLab.plotting.general 1.7.1 2010-06-15

MINOR UPDATES

  • create.boxplot: Renamed parameter 'ylimit' to 'ylimits' to standardize with other plotting functions
  • Updates to documentation and code formatting for standardization

BoutrosLab.plotting.general 1.7.0 2010-06-13

MAJOR UPDATES

  • Propagated graphics device changes to all plotting functions - enforced graphics type to 'cairo'

BoutrosLab.plotting.general 1.6.27 2010-06-11

MINOR UPDATES

  • create.heatmap: Added 'at' and 'colorkey.labels.at' parameters

BoutrosLab.plotting.general 1.6.26 2010-06-07

MINOR UPDATES

  • create.heatmap: Enforced graphics type to 'cairo' for all platforms

BoutrosLab.plotting.general 1.6.25 2010-06-02

MINOR UPDATES

  • panel.BL.bwplot: Updated documentation
  • create.scatterplot: Renamed 'lwdoutline' parameter to 'axis.lwd' for consistency in parameter names
  • create.scatterplot: Added parameters for fontfaces of x- and y-axis scales

BoutrosLab.plotting.general 1.6.24 2010-06-02

MINOR UPDATES

  • create.scatterplot: Updated to allow alteration of more plotting parameters and to match other plotting functions

BoutrosLab.plotting.general 1.6.23 2010-06-01

MINOR UPDATES

  • create.stripplot: Updated to allow for alteration of more plotting parameters

BoutrosLab.plotting.general 1.6.22 2010-05-27

MINOR UPDATES

  • create.boxplot: Updated to allow for alteration of more plotting parameters

BoutrosLab.plotting.general 1.6.21 2010-05-26

MINOR UPDATES

  • create.heatmap: Changed default colour.scheme from legacy parameter-handling
  • create.heatmap: Removed spurious warnings in legacy code and added error-handling for bad usage

BoutrosLab.plotting.general 1.6.20 2010-05-26

MINOR UPDATES

  • create.scatterplot: Added 'compression' parameter for tiff file customization

BoutrosLab.plotting.general 1.6.19 2010-05-25

MINOR UPDATES

  • create.heatmap: Allowed clustering of only one dimension at a time

BoutrosLab.plotting.general 1.6.18 2010-04-26

MINOR UPDATES

  • create.scatterplot: Added 'lwd' parameter for best-fit lines

BoutrosLab.plotting.general 1.6.17 2010-04-24

MINOR UPDATES

  • create.heatmap: Changed ordering of top covariates to match right covariates
  • create.heatmap: Changed axis tick-marks to be dynamic based on number of rows/columns in the heatmap

BoutrosLab.plotting.general 1.6.16 2010-04-23

MINOR UPDATES

  • create.scatterplot: Allowed for removal of axis-lines

BoutrosLab.plotting.general 1.6.15 2010-04-14

BUG FIXES

  • create.boxplot: Fixed colouring issues that arose when 'box.colour' argument was passed as a vector

MINOR UPDATES

  • panel.BL.bwplot: Added this function to fix colouring issues with lattice::panel.bwplot()

BoutrosLab.plotting.general 1.6.14 2010-04-12

MINOR UPDATES

  • create.heatmap: Added 'fill.colour' parameter for background
  • create.heatmap: Allowed specification of arbitrary colour-combinations

BoutrosLab.plotting.general 1.6.13 2010-04-11

MINOR UPDATES

  • create.heatmap: Added parameter for covariate-size

BoutrosLab.plotting.general 1.6.12 2010-04-09

MINOR UPDATES

  • create.heatmap: Allowed for plotting of arbitrarily large heatmaps when clustering is turned off

BoutrosLab.plotting.general 1.6.11 2010-04-09

MINOR UPDATES

  • create.boxplot: Removed pass-through parameterization because it can cause crashes when a fixed parameter is duplicated
  • create.boxplot: Allowed separate sizing of axis labels and axis scales

BoutrosLab.plotting.general 1.6.10 2010-04-02

MINOR UPDATES

  • create.boxplot: Renamed 'box.color' to 'box.colour' to match other variables
  • create.boxplot: Added 'symbol.cex' parameter to adjust outlier point size

BoutrosLab.plotting.general 1.6.9 2010-04-01

MINOR UPDATES

  • create.barplot: Parameterized label-sizes

BoutrosLab.plotting.general 1.6.8 2010-04-01

MINOR UPDATES

  • create.boxplot: Added 'box.color' parameter
  • create.boxplot: Updated to return a handle to plot object and added default values to input arguments
  • create.multiple.boxplots: Updated to get better memory efficiency

BoutrosLab.plotting.general 1.6.7 2010-03-31

MINOR UPDATES

  • create.barplot: Adjusted cex parameters
  • create.histogram: Updated to allow specification of type (percent, count, or density)
  • Cleaned up documentation to reduce warnings and be more explicit

BoutrosLab.plotting.general 1.6.6 2010-03-24

MINOR UPDATES

  • scientific.notation.2: Updated to allow proper handling of zeros

BoutrosLab.plotting.general 1.6.5 2010-03-15

MINOR UPDATES

  • create.heatmap: Updated to allow for adjustment of colour-range

BoutrosLab.plotting.general 1.6.4 2010-03-14

MINOR UPDATES

  • create.heatmap: Added selective plotting of right/top/left dendrograms
  • create.heatmap: Improved colour-palette selection by calculating the range of the data
  • create.heatmap: Allowed specification of main figure title
  • create.heatmap: Allowed separate output of a file and/or return of a trellis object
  • Enforced minimum version numbers on package dependencies

BoutrosLab.plotting.general 1.6.3 2010-03-14

MINOR UPDATES

  • create.heatmap: Added BlueWhiteYellow colour-scheme
  • create.heatmap: Updated to not run wit an invalid colour-scheme

BoutrosLab.plotting.general 1.6.2 2010-03-05

MINOR UPDATES

  • create.boxplot: Added option to plot or not plot outliers

BoutrosLab.plotting.general 1.6.1 2010-03-03

MINOR UPDATES

  • create.hexbinplot: Added new function to create hexbin plots
  • create.boxplot: Updated to control x- and y-axis tick sizes

BoutrosLab.plotting.general 1.5.3 2010-03-01

MINOR UPDATES

  • create.heatmap: Added ability to change legend size

BoutrosLab.plotting.general 1.5.2 2010-02-26

MINOR UPDATES

  • create.boxplot: Updated so that x-axis label does not overlap with x-axis ticks

BoutrosLab.plotting.general 1.5.1 2010-02-26

MINOR UPDATES

  • create.boxplot: Updated to be able to set label size

BoutrosLab.plotting.general 1.5.0 2010-02-25

MAJOR UPDATES

  • create.dotmap: Added new function to create dotmaps

MINOR UPDATES

  • create.scatterplot: Added examples

BoutrosLab.plotting.general 1.4.12 2010-02-24

MINOR UPDATES

  • create.scatterplot: Added parameters for plot-type, point/line size, colour, and symbol

BoutrosLab.plotting.general 1.4.11 2010-02-19

MINOR UPDATES

  • create.barplot: Fixed handling of clustering methods other than 'none' or 'diana'
  • create.heatmap: Allowed for column-wise covariates
  • create.heatmap: Allowed for any agglomerative clustering method available via hclust

BoutrosLab.plotting.general 1.4.10 2010-02-08

MINOR UPDATES

  • create.boxplot: Allowed for rotation of x-axis names

BoutrosLab.plotting.general 1.4.9 2010-02-06

MINOR UPDATES

  • create.stripplot: Added new function to create strip plot

BoutrosLab.plotting.general 1.4.8 2010-02-03

MINOR UPDATES

  • create.barplot: Added new function to create barplot

BoutrosLab.plotting.general 1.4.7 2010-02-01

MINOR UPDATES

  • create.boxplot: Updated to save figure directly and added example

BoutrosLab.plotting.general 1.4.6 2010-01-29

BUG FIXES

  • create.heatmap: Fixed bug in parameter-handling that introduced spurious warnings

BoutrosLab.plotting.general 1.4.5 2010-01-29

MINOR UPDATES

  • create.multiple.boxplots: Modified to remove build/check warnings
  • create.multiple.boxplots: Modified to ensure functionality when 'plot.names' input has less components than the 'data' input

BoutrosLab.plotting.general 1.4.4 2010-01-29

BUG FIXES

  • create.multiple.boxplots: Fixed error where \usage called wrong function name and one argument was missing in \arguments

MAJOR UPDATES

  • create.boxplot: Added new function to create boxplots

BoutrosLab.plotting.general 1.4.3 2010-01-28

MAJOR UPDATES

  • create.multiple.boxplots: Added new function to create multiple boxplots

BoutrosLab.plotting.general 1.4.2 2010-01-27

MINOR UPDATES

  • create.heatmap: Added ability to have clustered data without dendrograms

BoutrosLab.plotting.general 1.4.1 2010-01-27

MINOR UPDATES

  • create.heatmap: Added ability to handle different clustering algorithms and not plot dendrograms

BoutrosLab.plotting.general 1.4.0 2010-01-27

MAJOR UPDATES

  • create.histogram: Added function to create histograms

BoutrosLab.plotting.general 1.3.0 2010-01-26

MAJOR UPDATES

  • create.scatterplot: Added function to create scatterplots
  • scientific.notation.2: Added function to facilitate embedding of scientific notation inside other figures

BoutrosLab.plotting.general 1.2.0 2010-01-07

MAJOR UPDATES

  • scientific.notation: Added function to allow for proper scientific notation in plots

BoutrosLab.plotting.general 1.1.0 2010-01-07

MAJOR UPDATES

  • create.heatmap: Added function to create heatmaps

BoutrosLab.plotting.general 1.0.0 2010-01-06

MAJOR UPDATES

  • Initialized package for plotting functions
  • create.violin.plot: Added function to create violin plots

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BoutrosLab.plotting.general")

5.9.2 by Paul Boutros, a year ago


Browse source code at https://github.com/cran/BoutrosLab.plotting.general


Authors: Paul Boutros [aut, cre] , Jennifer Aguiar [ctb] , Ontario Institute for Cancer Research [cph] , The R Core Team [cph] , The R Foundation [cph] , Robert Gentleman [ctb] , Ross Ihaka [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports gtable, e1071, tools, gridExtra, MASS

Depends on lattice, latticeExtra, cluster, hexbin, grid

Suggests Cairo, knitr


See at CRAN