Question

Which package is best for a heatmap/image with sorting on rows only, but don’t show any dendrogram or other visual clutter (just a 2D colored grid with automatic named labels on both axes). I don’t need fancy clustering beyond basic numeric sorting. The data is a 39×10 table of numerics in the range (0,0.21) which I want to visualize.

I searched SO (see this) and the R sites, and tried a few out. Check out R Graphical Manual to see an excellent searchable list of screenshots and corresponding packages.

The range of packages is confusing – which one is the preferred heatmap (like ggplot2 is for most other plotting)? Here is what I found out so far:

• base::image – bad, no name labels on axes, no sorting/clustering
• base::heatmap – options are far less intelligible than the following:
• pheatmap::pheatmap – fantastic but can’t seem to turn off the
  dendrograms? (any hacks?)
• ggplot2 people use geom_tile, as Andrie points out
• gplots::heatmap.2 , ref – seems
  to be favored by biotech people, but way overkill for my purposes. (no
  relation to ggplot* or Prof Wickham)
• plotrix::color2D.matplot also exists

base::heatmap is annoying, even with args heatmap(..., Colv=NA, keep.dendro=FALSE) it still plots the unwanted dendrogram on rows.

For now I’m going with pheatmap(..., cluster_cols=FALSE, cluster_rows=FALSE) and manually presorting my table, like this guy: Order of rows in heatmap?

Addendum: to display the value inside each cell, see: display a matrix, including the values, as a heatmap . I didn’t need that but it’s nice-to-have.

Answer 1

With pheatmap you can use options treeheight_row and treeheight_col and set these to 0.