Depth plot + conos umap

khodosevichlab / CRMetrics

Summarization of CellRanger count metrics.

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Depth plot + conos umap #15

Closed HenriettaHolze closed 2 years ago

HenriettaHolze commented 2 years ago

[x] Make a histogram of depth over all samples to identify cells with low depth, x-axis is the number of UMIs, y-axis is frequency. Optional parameters: cut-off
to plot a vertical red line in the histogram
to return a data frame of cell IDs and True/False whether they are above the threshold
18
[x] colors the cells in UMAP by whether they are below the thresholds
[x] color the cells in UMAP by doublets, also see #16

rrydbirk commented 2 years ago

[x] Add function call to calculate UMAP W/O having to run plotUMAP

rrydbirk commented 2 years ago

I think we should simplify our plotting functions. We could remove plotUMAPDepth and include it in plotUmap, e.g. with parameter color.by = "depth" or "doublet". Otherwise, we could have plotDepth with type = "umap" or "histogram", same for doublets, etc.

Any thoughts?

rrydbirk commented 2 years ago

Fixed in d1824da