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kevinblighe / scDataviz

scDataviz: single cell dataviz and downstream analyses
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Feat/sample median heatmap #8

Closed JamesOpz closed 4 years ago

JamesOpz commented 4 years ago

This function takes as input the intitialized scToolkit object and splits the expression matrix into its respective samples using the "group" metadata slot. Uses the median marker expression across all cells for each smaple to produce a hierarchichal clustering heatmap using the "pheatmap" package. It can also take as argument a "feature", which represents a metadata slot, to annotate the heatmap with another experimental condition. Below is output without feature:

sample_heatmap_no_feature.pdf

and the output also with feature:

sample_heatmap_with_feature.pdf

JamesOpz commented 4 years ago

The function now works on the SingleCellExperiment object and is up to date with the master. I've updated the other fucntions, I just need to rebase the branches so they are up to date.

JamesOpz commented 4 years ago

I think that this branch has been rebased now and can be merged successfully.