Highlighting genes of interest in RNA-seq heatmap

[znasim09]

Hello everyone,

I was wondering whether its possible to make a heat map from cuffdiff output that highlights a few genes in a different color (or any other way). E.g., if I want to highlight 5-7 genes in a heat map containing ~400 genes.

Thanks in advance

[wdecoster]

That's very likely possible with ggplot2 in R (because everything is possible with ggplot2)

[thermophile]

I use heatmap3 in R. (hard as it is to believe there are a few things that ggplot doesn't do well, yet)

[znasim09]

@thermophile,
I made the heatmap using csHeatmap(myGenes,cluster='both') command. So how can I modify it to get clear differentiation of the expression pattern in different groups/samples in terms of colors? or even a dendogram can be helpful

[thermophile]

I've never used that package. I know that you can highlight cells and add dendograms using heatmap3. Go through their vignette to learn how

[SeqAn30]

Bioconductor package Heatplus provides options for gene/sample annotations for heatmaps.