R：哪个热图/图像在没有任何树状图的情况下得到行排序图？

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 39x10 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

使用pheatmap您可以使用选项treeheight_row和treeheight_col并将它们设置为0。

Answer 2

just another option you have not mentioned...package bipartite as it is as simple as you say

library(bipartite)
mat<-matrix(c(1,2,3,1,2,3,1,2,3),byrow=TRUE,nrow=3)
rownames(mat)<-c("a","b","c")
colnames(mat)<-c("a","b","c")
visweb(mat,type="nested")