Changes in version 1.0.13 (2025-06-05) o Trying to comply with CRAN policies Changes in version 1.0.12 (2019-01-04) o New option angle_col that allows to change the orientation of column labels Changes in version 1.0.11 o Now values outside of provided breaks correspond to highese/lowest supplied color (thanks Manuela Hummel) Changes in version 1.0.10 (2018-05-19) o Fixed the blank page issue for RMarkdown notebooks and printing heatmaps to pdf without using filename parameter o Can set color of NA now o Output now is a pheatmap object with same slots as previously, but it has also print and grid.draw functions (thanks Guangchuang Yu) Changes in version 1.0.9 o Now using pheatmap does not interfer with random seed anymore (thanks Simon de Bernard) Changes in version 1.0.8 (2015-12-11) Introduced changes by Tauno Metsalu o It is now possible to use hclust as an object o the display of annotation names can be controlled in more detail now Changes in version 1.0.7 (2015-07-02) o Trying to comply with CRAN policies Changes in version 1.0.6 o Added clustering_callback option to give more control over the hierarchical clustering Changes in version 1.0.5 o Fixed the continuous legend bug Changes in version 1.0.4 o Make the NA handling in parameters more intelligent Changes in version 1.0.3 o Make the NA handling more intelligent for annotations Changes in version 1.0.2 (2015-03-10) o Trying to comply with CRAN policies Changes in version 1.0.1 o Fixed small bug with gap calculation Changes in version 1.0.0 Major rewrite of pheatmap o 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 o 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. o Now it is possible to annotate rows of heatmaps in similar manner as it was possible with columns before. o Now it is possible to supply custom labels for rows and columns. o Added names to annotation tracks o Improved the overall appearance of the plot, concentrating on legends and annotation color schemes Changes in version 0.7.10 o Can set color to the values shown inside the cells. Changes in version 0.7.9 o Added option to show arbitrary values within cells, by giving a matrix to display_numbers parameter. Changes in version 0.7.8 o Made the dendrogram drawing faster Changes in version 0.7.7 (2013-09-19) o Fixed a bug related to calculating space for the column and row names. Made the documentation more readable o Added .Rbuildignore Changes in version 0.7.6 o Fixed a bug, where the color scales for scaled matrices were not centered to 0. Changes in version 0.7.5 o Minor bug fix Changes in version 0.7.4 (2012-11-22) o Minor bug fixes Changes in version 0.7.2 (2012-09-03) o Fixed some bugs introduced by changing the direction of plotting the y axis Changes in version 0.7.1 (2012-08-29) o Added option to modify labels of the color scale legend (legend_breaks and legend_labels) o Changed the direction of plotting to start from the top instead of bottom on y axis. Changes in version 0.7 (2012-08-13) o Added opportunity to show also the corresponding numeric values in the cells (see display_numbers parameter). o Added opportunity to show unused factor levels for column annotations in the legend (drop_levels parameter). o Changed the order how the rows are drawn when rows are not clustered. Before it started from the bottom, now from the top. o Changed legend positioning according to the presence of column names o The function now returns invisibly all the clusterings that it performed.