Question: SC3 how to customize plots ?
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11 months ago by
shaktirielland0 wrote:

Hello,

I'm trying SC3 for single cell data analysis and it is very useful so far.

I just have a question about plots : when plotting the consensus matrix with sc3_plot_consensus, cells can be annotated by using parameter "show_pdata" like in the provided example (https://bioconductor.org/packages/devel/bioc/vignettes/SC3/inst/doc/SC3.html#consensus-matrix) like so:

sc3_plot_consensus( sce, k = 3, show_pdata = c("cell_type1", "sc3_3_clusters") )

How can you specify custom colors for this additional information (in this example how to specify that we want specific color for each cluster, and not the automatic colors provided by SC3) ? Same question (and hopefully same answer) when plotting top marker genes with sc3_plot_markers(sce, k = 3) ?

Thanks,

S.

plot heatmap marker sc3 consensus • 266 views
modified 11 months ago by Vladimir Kiselev150 • written 11 months ago by shaktirielland0
Answer: SC3 how to customize plots ?
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11 months ago by
Sanger Institute, Cambridge, UK