Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-seq, RPKM and heatmap??? sdwy2008 RNA Sequencing 10 07-14-2011 11:41 PM
ncRNA heatmap with next gen sequencing NicoBxl Bioinformatics 2 11-23-2010 02:12 AM
'heatmap' tool Livi81 General 0 07-14-2010 04:07 PM
Bowtie and Color Space cutcopy11 SOLiD 9 02-05-2010 03:50 AM
direct mapping of color-space data against color-space begsch SOLiD 1 09-09-2009 10:25 PM

Thread Tools
Old 06-13-2011, 03:09 PM   #1
Junior Member
Location: Cambridge, MA

Join Date: Jun 2011
Posts: 7
Default R: heatmap color palette


I am using R to get the correlation matrix for some gene expression data. I have the correlation matrix, and I want to use a heatmap to visualize it.

I would like to use a different color palette than the default from the heatmap, something ranging from blue to red, what is the easiest way to do this?

Thanks in advance.
akolman is offline   Reply With Quote
Old 06-13-2011, 04:14 PM   #2
--Site Admin--
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358

Maybe this will help. You can set the high:low colors at will:
ECO is offline   Reply With Quote
Old 06-14-2011, 06:43 AM   #3
Senior Member
Location: Kansas City

Join Date: Mar 2008
Posts: 197

You can use RColorBrewer... there's a number of pre-made palettes, one of which is called RdBu and goes from Red to White to Blue.


You can also use something like

to get more creative with your colors.
mgogol is offline   Reply With Quote
Old 06-14-2011, 09:47 AM   #4
Genome Informatics Facility
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default R heatmap.2

I am a big fan of heatmap.2 in R that you can download from CRAN gplots.

heatmap.2(as.matrix(your data),col =

This color code is also color blind friendly.
severin is offline   Reply With Quote
Old 06-15-2011, 08:30 AM   #5
Senior Member
Location: Woodbridge CT

Join Date: Oct 2008
Posts: 231
Default A handy guide to picking colors to work in gray scale

For many cases in facilitating the further use of published data presented in color, here is a technique for making your color choices so they live on in black and white 2nd gen copy.

See illustration:
"To pick colors easily discernible from each other, whether in color or converted to grayscale, spiral through the color wheel."

Bang Wong Nature Methods 7:573 (2010)
doi: 10.1038/nmeth0810-573
Joann is offline   Reply With Quote
Old 06-16-2011, 12:51 PM   #6
Deli Çoban
Junior Member
Location: evde

Join Date: May 2011
Posts: 6

Originally Posted by ECO View Post
Maybe this will help. You can set the high:low colors at will:
Really thanks for your valuable contribution..
Deli Çoban is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:50 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO