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Question: sc3_plot_expression, colour labels
1
gravatar for cfustero
5 months ago by
cfustero20
Madrid (Spain)
cfustero20 wrote:

Hi,

I have been using the "SC3" R package to analyse single cell expression data. We expect to find four different groups of cells within our data, so I've included a column corresponding to our cell labels.
When using the sc3_plot_expression, our cell labels are coloured automatically, but the colours are really similar between each other and it's hard to discern between groups. Is there any parameter I can use to manually adjust the label colours?

Thanks a lot!
Coral

ADD COMMENTlink modified 5 months ago by Vladimir Kiselev120 • written 5 months ago by cfustero20
2
gravatar for Vladimir Kiselev
5 months ago by
Sanger Institute, Cambridge, UK
Vladimir Kiselev120 wrote:

Hi,

Unfortunately, it is not possible through sc3_plot_expression itself. However, since all heatmaps in SC3 are based on the pheatmap package, you can use the source code of sc3_plot_expression and add some manual colour annotations to it via pheatmap arguments.

So if object is your scater object and k is the number of clusters (4 in your case) then you can plot the expression matrix (without coloured cell labels) using this code:

library(scater)
library(SC3)
library(pheatmap)

hc <- object@sc3$consensus[[as.character(k)]]$hc
dataset <- get_exprs(object, "exprs")

pheatmap(
    dataset, 
    cluster_cols = hc, 
    kmeans_k = 100, 
    cutree_cols = k, 
    show_rownames = FALSE, 
    show_colnames = FALSE
)

Then you will need to add both annotation_col and annotation_colors arguments to the last pheatmap call. For mored details and examples on how to do it please refer to the pheatmap documentation using:

?pheatmap
ADD COMMENTlink modified 5 months ago • written 5 months ago by Vladimir Kiselev120
1

Thanks a lot for your quick response, Vladimir!

ADD REPLYlink modified 5 months ago • written 5 months ago by cfustero20
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