SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
negative log color value legend in R startcodon Bioinformatics 2 08-21-2012 10:44 PM
DESeq Heatmaps sjv3 RNA Sequencing 3 06-15-2012 11:00 AM
generating heatmaps of repeat density in genome sequences bobvanburen Bioinformatics 1 05-10-2012 07:15 PM
help with a heatmap with deseq - legend? vebaev Bioinformatics 3 03-03-2012 09:39 AM
EdgeR: Heatmaps polsum Bioinformatics 5 02-04-2012 11:47 AM

Reply
 
Thread Tools
Old 07-30-2013, 10:10 AM   #1
ashuchawla
Member
 
Location: san diego

Join Date: Jan 2012
Posts: 38
Default legend for heatmaps

I am trying to create a heat map of genes with log2foldchange values. Following is my code,

pdf("fold_change_heatmap_top_100.pdf" , height=20, width=15)
x <- as.matrix(fold_change_genes[fold_change_genes$gene %in% top_100 , c(2,3,4)])
heatmap(x, margins = c(6,6) , cexCol=2 )
dev.off()

But I cannot see the legend for this plot. I am not sure how draw that..Could anyone please help me? I cannot use gplots::heatmap.2 as it is not installed on the cluster I am working on yet. Please suggest something.

Thanks,
Ashu
ashuchawla is offline   Reply With Quote
Old 07-30-2013, 10:40 AM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 666
Default legend for heatmaps

have you tried typing '?heatmap' to get the help page for
the R function heatmap.

That should give you a list of the parameters you can use with heatmap().
mastal is offline   Reply With Quote
Old 07-30-2013, 10:45 AM   #3
ashuchawla
Member
 
Location: san diego

Join Date: Jan 2012
Posts: 38
Default

Yes I have and it doesnt tell me anything
ashuchawla is offline   Reply With Quote
Old 07-31-2013, 07:55 AM   #4
paolo.kunder
Member
 
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
Default

why don't you try

heatmap.2 in library gplots

Last edited by paolo.kunder; 07-31-2013 at 07:59 AM.
paolo.kunder is offline   Reply With Quote
Old 04-09-2014, 03:30 AM   #5
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Default

can somebody answer this trouble, please?
http://seqanswers.com/forums/showthr...ight=heatmap.2
jp. is offline   Reply With Quote
Reply

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 07:17 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO