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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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How are top.n cell types selected in SingleR.DrawHeatmap #29

Closed danshu closed 5 years ago

danshu commented 5 years ago

Hi,

I want to visualize top 30 most abundant cell types in a heat map so I set top.n=30 in SingleR.DrawHeatmap. However, some top cell types (such macrophage) are missing from the heatmap. So How are top.n cell types selected in SingleR.DrawHeatmap?

Best, Danshu

dviraran commented 5 years ago

Hi,

These are the top scored cell types. Apparently, macrophages are not top ranked cell types.

You can use the field types.use to present whichever cell types you want. Get the list of cell types from the col names of the scores matrix and choose whatever subset you want.

Best, Dvir

danshu commented 5 years ago

Thanks!