SC3 how to customize plots ?
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@shaktirielland-18608
Last seen 3.8 years ago

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.

SC3 plot consensus marker heatmap • 711 views
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Entering edit mode
Last seen 3.5 years ago
Sanger Institute, Cambridge, UK

Hi, sorry for the late reply. For heatmap plots SC3 is using the pheatmap package (https://cran.r-project.org/web/packages/pheatmap/index.html). It looks like it's still not possible to control the colour palettes in that package, but please have a better look there and if there is could you please submit a pull request here: https://github.com/hemberg-lab/SC3