CODEWITHSUNDEEP
imagerheatmap
smci
smci

Reputation: 33970

R: Which heatmap/image to get row-sorted plot without any dendrogram?

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::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.

Upvotes: 11

Views: 4707

Answers (2)

Raivo Kolde
Raivo Kolde

Reputation: 739

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

Upvotes: 6

user1317221_G
user1317221_G

Reputation: 15461

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")

Upvotes: 1

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