heatmap column(sample) names disordered
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10 months ago
ziziqolo ▴ 10

Hi dear biostar community,

I have a problem with my heatmap output. I want to draw a heatmap of 45 topvar genes for 52 samples. but my column (sample) names are shown disordered. (e.g. f1d#num is femal-1dpi-disease, and f1c#num is female-1dpi-control) as you can see, column have not any meaningful order. what can I do?

many thanks also I added my output image

heatmap.2 deseq2 Studio R • 486 views
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Order of samples is based on sample (column) clustering, present on the top of image. You can turn off clustering to sort sample names of your choice, on heatmap.

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Would you please tell me more how I can turn off clustring and then cluster by my choice? I'm a beginner unfortunately. Thank you.

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I am not sure how above image is done. Based on your tags, you seem to have used heatmap.2 from gplots

try this:

$ heatmap.2(x, dendrogram="none", Colv = F)

x being object for drawing.

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so sorry but another question came up for me. Is there ay way to both have ColV = F and dendrogram="column"?

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As far as I know, no. You can try doing that, program throws an error. It also doesn't make sense if one thinks it over.

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