R heatmaply and pheatmap output

问题

I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same color output I get using the pheatmap package. Therefore, I would like the two commands to produce the same ouput:

heatmaply (scale (mtcars))
pheatmap  (scale (mtcars))

Is there a way to do this? Thanks in advance. Arturo

回答1:

You can use formals() to get the default color argument of pheatmap().

formals(pheatmap)$color
# colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100)

Then set the color argument of heatmaply() to the same one:

col <- colorRampPalette(rev(RColorBrewer::brewer.pal(n = 7, name = "RdYlBu")))(100)
heatmaply(scale(mtcars), colors = col, grid_color = "grey60")

• The color function brewer.pal() is from the RColorBrewer package, so you need to install and load it with :: or library() in advance.
• grid_color in heatmaply() is corresponding to border_color in pheatmap().

来源：https://stackoverflow.com/questions/61931334/r-heatmaply-and-pheatmap-output