Seurat: Customize colors for DoHeatmap function in v3

Created on 10 Jan 2019 · 7Comments · Source: satijalab/seurat

Hello,
I really appreciate your efforts to make such useful tool for single cell RNA seq.
I've been using v2 for the whole time and now adjusting to v3.

I've found that DoHeatmap function has changed a bit. Previously, we were able to set colors manually through col.low ~col .high, but I've found it's missing in v3. Is it deprecated?

If so, how can I set colors manually for DoHeatmap function?

Source

MJ-Yang

Most helpful comment

Hi,

Since DoHeatmap returns a ggplot object in Seurat v3, you can manipulate the colors by specifying the color scale. For example

library(ggplot2)
DoHeatmap(object = pbmc_small) + scale_fill_gradientn(colors = c("blue", "white", "red"))

You can also easily apply color schemes provided by other packages, such the viridis color palettes.

library(viridis)
DoHeatmap(object = pbmc_small) + scale_fill_viridis()

andrewwbutler on 10 Jan 2019

👍4

All 7 comments

Hi,

Since DoHeatmap returns a ggplot object in Seurat v3, you can manipulate the colors by specifying the color scale. For example

library(ggplot2)
DoHeatmap(object = pbmc_small) + scale_fill_gradientn(colors = c("blue", "white", "red"))

You can also easily apply color schemes provided by other packages, such the viridis color palettes.

library(viridis)
DoHeatmap(object = pbmc_small) + scale_fill_viridis()

andrewwbutler on 10 Jan 2019

👍4

Hi, I think it's currently not possible to change the color of group bar, right?

DoHeatmap(object = pbmc_small) + scale_color_manual(values=cbPalette)

lima1 on 14 Mar 2019

No, unfortunately it's not currently possible to change those colors though we would welcome a PR for that feature if anyone's interested in implementing.

andrewwbutler on 18 Mar 2019

Single a google search defaults to this I thought i'd add this in case someone would be interested

DoHeatmap

group.colors = c("red", "blue") adds colors to the bar.

Dragonmasterx87 on 9 Oct 2019

👍1

Does anyone know if you can sort the groups (columns) in the heatmap specifically in doheatmap?

lwhitmore on 6 Feb 2020

@lwhitmore You can do this by changing the order of levels of the variable that you want to sort by.

levels(factor(object@variable_to_sort))
> levels: 1,2,3
object@variable_to_sort <- factor(object@variable_to_sort, levels=c(3,2,1))
levels(object@variable_to_sort)
> levels: 3,2,1

kaizen89 on 16 Mar 2020

Follow the @andrewwbutler idea , we can do the following

mapal <- colorRampPalette(RColorBrewer::brewer.pal(11,"RdBu"))(256)
DoHeatmap(pbmc_small, 
          angle = 90,size = 3)+
  scale_fill_gradientn(colours = rev(mapal))