Re: [R] heatmap-changing column or row names

From: Moreno Ignazio Coco <M.I.Coco_at_sms.ed.ac.uk>
Date: Thu, 29 May 2008 11:04:33 +0100

Hi Kevin,

thanks a lot for the advices. The first suggestion worked, overall, I have to find a way to scale the names/numbers on the interval considered. But it was the good way to look at the problem. The second suggestion didn't really work. It is not a problem of custom fitting, it is more where in the plot, zero is centered. If I say

abline(v=0)

it produces a vertical line much more right on the x axis than the actual 0. It is a problem of where the axis of the plots are set and they don't seem to match the layout of the heatmap. Any suggestion on this?

Moreno

Quoting "Kevin J. Thompson" <kthomps7_at_gmu.edu>:

>
>
> would this work for you?
>
>> cl2=c(rep('',4500))
>> for (i in seq(500,4500,by=500)){
> + cl2[i]=as.character(i)}
>>
>> heatmap(x, labCol=cl2)
>
> you might have to custom fit the lines
>
>> d=seq(.2,.8,by=.1)
>> abline(v=d)
>
> hope it helps,
> kt
>
> ----- Original Message -----
> From: Moreno Ignazio Coco <M.I.Coco_at_sms.ed.ac.uk>
> Date: Wednesday, May 28, 2008 12:55 pm
> Subject: [R] heatmap-changing column or row names
>
>> Dear R Community,
>>
>> I am trying to create an heatmap for the following set of data:
>>
>> ##example of data matrix
>> o4
>> V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18
>> green 27 28 29 29 28 28 26 25 25 23 23 22 22 21 21 22 22 22
>> yellow 6 8 8 7 7 7 6 6 6 7 7 7 6 6 6 6 6
>> 5
>> red 15 15 15 15 15 15 14 13 12 11 12 10 9 8 7 6 8
>> 9
>> pink 11 11 11 11 11 10 12 11 13 14 14 15 15 14 14 17 17 17
>> blue 17 15 15 16 17 17 17 17 18 18 18 19 20 20 20 21 22 21
>>
>> the column names are timepoints 450 in total. When I run the
>> heatmap code:
>>
>> x <- as.matrix(o4)
>> ramp <- colorRamp(c("yellow","green","blue"))
>> cv<-rgb( ramp(seq(0, 1, length = 83)), max = 255)
>>
>> heatmap(x, col = cv, Colv=NA, Rowv=NA,xaxt="n", yaxt="n",
>> scale="column", margins=c(5,10), labCol=NA,xlab = "Time", ylab=
>> "Colors",main = "")
>>
>> I have quite few problems to change the column names. Being 450
>> timepoints too many to be readable on the plot, I wanted to
>> reduce/scale them to, let say 45. So, as you can see from the code
>>
>> above, I have removed the x and y, row and column information.
>> Then I have tried to create a new name vector:
>>
>> ##create col vector to add names
>>
>> Colname<-as.character(seq(0,4500,500))
>>
>> ##putting it as arguments of (labCol=Colname, in the heatmap function)
>>
>> but this solution didn't work. It looks like as it cannot find the
>>
>> exact point on the axis where to stick the label in and it
>> clutters
>> all the datapoint on the same spot without being able to unfold it.
>>
>> Therefore I have tried to introduce an axis:
>>
>> axis(1, at=seq(0,450,1),line=1)
>>
>> and then adding some text on top
>>
>> mtext(paste(seq(0,4500, 250),sep=""),side=1,
>> at=seq(0,450,25),line=2,cex=0.6,las=1)
>>
>> also this way didn't work out. Actually, it has created a kind of
>> axis
>> but the zero of it was aligned to the middle of the plot. So, it
>> was
>> completely shifted.
>> That was my first problem.
>>
>> Second small problem.
>> I am trying to mark on the heatmap some crucial timepoints. I
>> wanted
>> to do it by adding a straight abline on the heatmap plot
>>
>> abline(v=80,col=green)
>>
>> but also this doesn't seem to have any result
>> It seems that it is quite difficult to add any information to the
>> heatmap, but perhaps some of you might know how to do it.
>>
>> Many thanks in advance
>>
>> Moreno
>>
>>
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.htmland provide commented, minimal, self-contained,
>> reproducible code.
>>
>
>

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

______________________________________________
R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Received on Thu 29 May 2008 - 11:53:55 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 29 May 2008 - 12:30:40 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive