plotYields {CATALYST} | R Documentation |
Plots the distribution of barcode separations and yields upon debarcoding as a function of separation cutoffs. If available, currently used separation cutoffs as well as their resulting yields will be indicated in the plot.
plotYields(x, which = 0, out_path = NULL, out_name = "yield_plot")
x |
|
which |
0, numeric or character. Specifies which barcode(s) to plot.
Valid values are IDs that occur as row names of |
out_path |
character string. If specified,
yields plots for all barcodes specified via |
out_name |
character strings specifying
the output's file name when |
The overall yield that will be achieved upon application of the specified set of separation cutoffs is indicated in the summary plot. Respective separation thresholds and their resulting yields are included in each barcode's plot. The separation cutoff value should be chosen such that it appropriately balances confidence in barcode assignment and cell yield.
a list of ggplot
objects.
Helena L Crowell helena.crowell@uzh.ch
Zunder, E.R. et al. (2015). Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature Protocols 10, 316-333.
# construct SCE & apply arcsinh-transformation data(sample_ff, sample_key) sce <- prepData(sample_ff) # deconvolute samples & estimate separation cutoffs sce <- assignPrelim(sce, sample_key) sce <- estCutoffs(sce) # all barcodes summary plot plotYields(sce, which = 0) # plot for specific sample plotYields(sce, which = "C1")