Adding box plot for gene expression to complexheatmap
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10 months ago
A ★ 3.9k

Hi

I have a complexheatmap like this save in object hm

I have RPKM values for these 11 genes for Responders (n=9) and Non responders(n=24) groups

I want to show the difference of RPKM between two groups as a side box plot (or violin)

I have tried this

head(df[1:5,1:5])
1        2        3         4        5
1 2.863344 1.898928 3.478697 2.3757564 2.135660
2 4.212727 2.463784 7.684164 1.9982669 4.112562
3 2.272057 1.066807 1.308542 0.7091228 4.606245
4 3.225457 1.358011 2.204351 2.1995727 5.025283
5 2.766198 1.628747 2.806077 1.4850733 3.077352
>

> dim(df)
[1] 11 33
> class(df)
[1] "data.frame"
>

.boxplot = anno_boxplot(df, which = "row")
ha_mix_right = HeatmapAnnotation(violin = .violin, bxplt = .boxplot,
which = "row", width = unit(4, "cm"))

hm+ha_mix_right


Which gives this

But by this we can not say if for instance RPKM values in CCND1 is higher in non-responders (I have already checked the differences between groups for these genes so I know the direction of expression level)

I also tried this but no success

Is these any way to show that here?

Thank you for any help to achieve this

r complexheatmap • 541 views
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A, Difference in FPKM/RPKM is not really something meaningful. If you still wish to show that, you should plot a scaled version of the difference. log2(Responder_RPKM/NonResponder_RPKM) would show if Responder is higher or lower than NonResponder. Don't call it Fold Change or make a statistical statement though.

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But people for the same data set done comparison and published that

I have checked the difference which is significant for some genes but I don't know how to visualize that here

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You know what, your results could be significant/published - I'm no expert on your data or journals' criteria. In any case, log2 fold change is something you can plot, and maybe only plot those for significant differences.