How to generate a similar heatmap?

Question

[datanerd]

Hi all,

I was wondering how to generate heatmap as in here

The colors inside the heatmap is confusing - how do a give colors to the separate dataset type- methylation , copy number etc?

Thanks in advance! Mmata

[WouterDeCoster]

As in what? Something is missing from your post ;)

[Devon Ryan]

The figure you linked to was likely made with heatmap.3 in R, for whatever that's worth.

[datanerd]

Thanks Devon. Iam using heatmap.plus (but should be similar) The thing that I dont understand is the color coding for different columns inside the heatmap. We usually use a colorscale for expression range, but this one is a binary matrix- so not sure how to show the colors for each type. Please let me know of any suggestions.

[igor]

They have the actual heatmap, but then they also have group labels in different colors.

[Devon Ryan]

As Igor said, the binary coloring is for group designations.

Answer 1

[natasha.sernova]

Look at this post.

Individual colors for heatmaps using ngsplot

deepTools explain different colors. http://deeptools.readthedocs.org/en/latest/content/tools/plotHeatmap.html

This article below explains what you want - colors for methylation in different samples, etc

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220495/figure/f2/

See their gallery, they provide some code inside.

http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions

[natasha.sernova]

It was my comment, I unsuccessfully changed it to a probable answer. Sorry if I did something wrong.

[datanerd]

Thanks Natasha.. I will look into it.