Heatmap R: how to remove dashed lines

Question

I'm new to heatmap. I've data which looks like:

Dat       A        B        C        D        E
A    100       30.3      0       55.71    45.78
B     12.85   100       72.85    12.64    98.51
C      0       27.85   100       82.28     3.07
D     23.71    30.64    40.28   100        6.33
E     25.25    85       52.36    36.33   100

R code:

pdf("hh.pdf")
library(gplots)
data = read.table("file.txt", header=T, row.names=1)
heatmap.2(as.matrix(data))
dev.off()

When I plot heatmap with above data, it is Okay, with those grid lines. But when I get row count as 100 or in that range, plot is barely visible. Plot is covered with dash-dash vertical lines.
I want to get rid of those annoying lines. I've saved in .png format, but again, I get same lines.

I have checked heatmap.2 (gplots package) - how to remove annoying lines in some cells?

Using R 3.0.2

@bluefeet : Well, I agree that it was kind of a lame question, but the referenced question and answer was NOT a duplicate. — IRTFM, Aug 12 '14 at 03:22
Wow! That was unsuspected behavior. Apparently I have the authority reopen questions with one vote. — IRTFM, Aug 12 '14 at 03:25
@BondedDust The user posted an answer [below](http://stackoverflow.com/a/25253809/426671) with a link to another SO question stating "Got it". That points out that this is a duplicate which was why I closed it. — Taryn, Aug 12 '14 at 10:28
Right, but neither of the answers mentioned `trace` or `tracecol` which were the parameters that controlled the "gridlines that were the nub of the question. The other answers involved color palettes. — IRTFM, Aug 12 '14 at 14:22

score 5 · Accepted Answer · answered Aug 11 '14 at 23:20

 pdf("hh.pdf")
 library(gplots)
 data = read.table(text="Dat       A        B        C        D        E
 A    100       30.3      0       55.71    45.78
 B     12.85   100       72.85    12.64    98.51
 C      0       27.85   100       82.28     3.07
 D     23.71    30.64    40.28   100        6.33
 E     25.25    85       52.36    36.33   100", header=T, row.names=1)

 heatmap.2(as.matrix(data), tracecol=NA)

score 2 · Answer 2 · answered Jan 05 '19 at 14:42

2

I would suggest also to use the package "pheatmap" as follows:

pheatmap(as.matrix(data)).

It is much more powerful than ggplots heatmap.2.

answered Jan 05 '19 at 14:42

M Sabry Sarhan

21
1

1

Having struggled with heatmap.2 I've now moved over to pheatmap. Thanks for this suggestion. – Anthony Nash Jun 11 '19 at 08:54

score 0 · Answer 3 · edited May 23 '17 at 12:31

0

Got it:

pdf("test.pdf")
data = read.table("srg.txt", header=T, row.names=1) 
heatmap.2(as.matrix(data), dendrogram=c("row"),density.info="none", trace="none",symm=T)
dev.off()

How to change heatmap.2 color range in R?

edited May 23 '17 at 12:31

Community

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1

answered Aug 11 '14 at 23:07

Death Metal

830
3
9
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Heatmap R: how to remove dashed lines

3 Answers3