Pretty Heatmaps

Implementation of heatmaps that offers more control over dimensions and appearance.


Version 1.0.12

  • New option angle_col that allows to change the orientation of column labels

Version 1.0.11

  • Now values outside of provided breaks correspond to highese/lowest supplied color (thanks Manuela Hummel)

Version 1.0.10

  • Fixed the blank page issue for RMarkdown notebooks and printing heatmaps to pdf without using filename parameter
  • Can set color of NA now
  • Output now is a pheatmap object with same slots as previously, but it has also print and grid.draw functions (thanks Guangchuang Yu)

Version 1.0.9

  • Now using pheatmap does not interfer with random seed anymore (thanks Simon de Bernard)

Version 1.0.8

Introduced changes by Tauno Metsalu:

  • It is now possible to use hclust as an object
  • the display of annotation names can be controlled in more detail now

Version 1.0.7

Trying to comply with CRAN policies

Version 1.0.6

Added clustering_callback option to give more control over the hierarchical clustering

Version 1.0.5

Fixed the continuous legend bug

Version 1.0.4

Make the NA handling in parameters more intelligent

Version 1.0.3

Make the NA handling more intelligent for annotations

Version 1.0.2

Trying to comply with CRAN policies

Version 1.0.1

Fixed small bug with gap calculation

Version 1.0.0

Major rewrite of pheatmap.

  • Internally pheatmap uses now gtable package and returns the gtable object that gives more flexibility in editing the figure or combining it with other plots
  • Introduced the opportunity to separate parts of heatmap using gaps. This can be achieved using gaps_col and gaps_row parameter when the corresponding dimension is not clustered. Alternatively cutree_row and cutree_col introduce the gaps based on the clustering.
  • Now it is possible to annotate rows of heatmaps in similar manner as it was possible with columns before.
  • Now it is possible to supply custom labels for rows and columns.
  • Added names to annotation tracks
  • Improved the overall appearance of the plot, concentrating on legends and annotation color schemes

Version 0.7.10

Can set color to the values shown inside the cells.

Version 0.7.9

Added option to show arbitrary values within cells, by giving a matrix to display_numbers parameter.

Version 0.7.8

Made the dendrogram drawing faster

Version 0.7.7

Fixed a bug related to calculating space for the column and row names. Made the documentation more readable

Added .Rbuildignore

Version 0.7.6

Fixed a bug, where the color scales for scaled matrices were not centered to 0.

Version 0.7.5

Minor bug fix

Version 0.7.4

Minor bug fixes

Version 0.7.2 and 0.7.3

Fixed some bugs introduced by changing the direction of plotting the y axis

Version 0.7.1

  • Added option to modify labels of the color scale legend (legend_breaks and legend_labels)
  • Changed the direction of plotting to start from the top instead of bottom on y axis.

Version 0.7

  • Added opportunity to show also the corresponding numeric values in the cells (see display_numbers parameter).
  • Added opportunity to show unused factor levels for column annotations in the legend (drop_levels parameter).
  • Changed the order how the rows are drawn when rows are not clustered. Before it started from the bottom, now from the top.
  • Changed legend positioning according to the presence of column names
  • The function now returns invisibly all the clusterings that it performed.

Reference manual

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1.0.12 by Raivo Kolde, 6 months ago

Browse source code at

Authors: Raivo Kolde

Documentation:   PDF Manual  

GPL-2 license

Imports grid, RColorBrewer, scales, gtable, stats, grDevices, graphics

Imported by ADAPTS, CB2, CINNA, CytobankAPIstats, DEVis, EcoGenetics, FAMILY, FateID, MetaIntegrator, MoonFinder, NPflow, RaceID, SCORPIUS, clustDRM, deTS, omics, psSubpathway, qiimer, statVisual, timeSeq.

Depended on by Canopy, KOGMWU, LncMod, MM2S.

Suggested by QuantNorm, diverse, eclust, mixdir, sigminer.

See at CRAN