[R] heatmap.2 questions

[Ryan van Laar]

I'm using this code to create a heatmap of expression data and indicate a
specific column of data, post clustering:

#Generate heatmap:
heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none",
col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1,
margin=c(5,5), scale="row", key=FALSE)

I have two problems that I'm hoping i can get some pointers on:

1. The column I want to indicate with a yellow line is column #1 in the
matrix, pre-clustering. How can I determine its position post-clustering, so
I can instruct the heatmap code to move the yellow 'sep' line to this
position?

2. The intensity of the colours is very dull and I cannot figure out how to
increase the contrast (a la Treeview). I have attached two images (not sure
if this is allowed), one being the image as it comes out from the code
above, and the other ("...copy.png") being how I would actuallt like it to
look. I adjusted the levels in photoshop to get this second image.

The data is log2 scale gene expression data (single channel), and scaled
with this command:

L3data_med<- scale(t(L3dataonly), center = TRUE)
> L3data_med2<-t(L3data_med)
>

...to median (mean?) centre the rows, prior to clustering.

Thanks in advance,

Ryan
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