[R] heat map labeling

[Angela]

Hi Jim,

Thank you, that definitely reduced it but there are still about 600 genes, so too many to label. It does make the heat map itself look cleaner. Maybe labeling isn't necessary for the heat map?

-Angela
--------------------------------------------
On Fri, 8/28/15, Jim Lemon <drjimlemon at gmail.com> wrote:

 Subject: Re: [R] heat map labeling

 Cc: "r-help mailing list" <r-help at r-project.org>
 Date: Friday, August 28, 2015, 6:16 AM

 Hi
 Angela,Assuming the above data frame is named
 angela.df:
 angela.mat<-as.matrix(angela.df[,2:3])angela.mat<-angela.mat[apply(angela.mat,1,function(x)
 all(x) > 0),]
 will remove all of the rows
 that have contain at least one zero.
 Jim

 On Fri, Aug 28, 2015 at
 9:00 AM, Angela via R-help <r-help at r-project.org>
 wrote:
 Hello,



 I have a dataset of 985 genes, looks something like the ones
 below. I want to label only those with the high intensities,
 since labeling all doesn't show up. Is there a way to do
 that? If not, is there a way to pull out the highest ones
 (say, highest 50, or those above X amount) and only show
[[elided Yahoo spam]]



 -Angela



 Z transforming gives all cells the same value, just + or -
 (for example, all have 0.5 and -0.5). The researchers want
 the actual values used.



 Gene   var1       var2

 A       8000000 0

 B       250000  300000

 C       750000  2000000

 D       0               0

 E       4000000 6000000

 E       5000000 700000

 E       1000000 1000000

 F       6000000 6000000

 F       700000  827460

 G       420930  400000

 H       0               0

 H       1000000 1000000

 I       700000  600000

 J       0               700000

 K       0               0

 L       200000  500000

 L       1000000 3000000



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