HeatMap

Question

[barix]

I have a question regarding heat map legend. What does mean 0 to 1? Is this a z-score? How to label it?

Thanks!!

[Ram]

The values in the heatmap go from 0 (white) to 1 (red). Given how little context you've given us here, this is the most we can tell you. If you were to share where this heatmap is from (and maybe read the source a little while you're at it), you could get more clarity on what the values themselves mean.

[Michael]

Context please. You ned to consult the original publication, check the figure legend and the methods section, it looks like it could be a z-score of some kind, it could be anything really, it is impossible to know without context.

[barix]

It is from this tutorial dittoSeq

[Michael]

So type:

?dittoHeatmap

and check what the parameter scaled.to.max does. It looks like it just does row scaling by x/row.max, that's not really a z-score.

[barix]

Thank you. I'm not bioinformatician, just looking for an explanation how to label the legend (gene expression, z-score...)?

Answer 1

[jared.andrews07]

If you'd like a z-score, you can set scale = "row" and scaled.to.max = FALSE. Otherwise, it just scales to the mostly highly expressed cell/sample for each feature (so the highest sample would be set to 1). If I were to label that, I'd probably just label it "Max Expression".