[R] heatmap-changing column or row names

[Moreno Ignazio Coco]

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.
>>
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>>
>
>



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