Or in other words, you can add multiple pheatmapsĪnd annotations. pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row,ĬomplexHeatmap::pheatmap() returns a Heatmap object, so it can be added with You can split the heatmap by rows or by columns, which is a unique feature of ComplexHeatmap. ) pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, Rownames(annotation_col) = paste('Test', 1:10, sep = '') How to set these data frames and color list if you are a pheatmap user). The next one is an example for setting annotations (you should be familiar with

Some other visual difference which you can find in the “Comparisons” section in this post. pheatmap(test) # this is ComplexHeatmap::pheatmapĮverything looks the same except the style of the heatmap legend. Rownames(test) = paste('Gene', 1:20, sep = '')Ĭalling pheatmap() (which is now actually ComplexHeatmap::pheatmap()) generatesĪ similar heatmap as by pheatmap::pheatmap(). The documentation of pheatmap::pheatmap() function. The colors for individual values are automatically interpolated.įirst we load an example dataset which is from the “Examples” section of You can use the same setting of color in ComplexHeatmap::pheatmap(), but youĬan also simplify it as: ComplexHeatmap::pheatmap(mat,Ĭolor = rev(brewer.pal(n = 7, name = 'RdYlBu')) In pheatmap::pheatmap(), the color argument is specified with a long color vector,Ĭolor = colorRampPalette(rev(brewer.pal(n = 7, name = 'RdYlBu')))(100) The usage of remaining arguments is exactly the same as in pheatmap::pheatmap(). Some arguments in pheatmap::pheatmap() are disabled and ignored in this translation, Rerun your pheatmap code and it will automatically and nicely convert to the Which means, you don’t need to do any adaptation on your pheatmap code, you just By doing this, the most significant improvement is now youĬan add multiple pheatmaps and annotations (defined byĬomplexHeatmap::pheatmap() includes all arguments in pheatmap::pheatmap(), Parameters in ComplexHeatmap::Heatmap(), which means, it converts a pheatmap Which actually maps all the parameters in pheatmap::pheatmap() to proper From version 2.5.2 ofĬomplexHeatmap, I implemented a new ComplexHeatmap::pheatmap() function Pheatmap is a great R package for making heatmaps, inspiring a lot of other

Shadow complex map legend