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

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

5.9.2 by Paul Boutros, 10 months 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

BoutrosLab.plotting.general

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