plotEvents {CATALYST} | R Documentation |
Plots normalized barcode intensities for a given barcode.
plotEvents(x, ...) ## S4 method for signature 'dbFrame' plotEvents(x, which = "all", n_events = 100, out_path = NULL, name_ext = NULL)
x |
a |
... |
optional arguments. |
which |
|
n_events |
numeric. Specifies number of events to plot. Defaults to 100. |
out_path |
character string. If specified, outputs will be generated here. |
name_ext |
character string. If specified, will be appended to the file name. |
Plots intensities normalized by population for each barcode specified
by which
: Each event corresponds to the intensities plotted on a
vertical line at a given point along the x-axis. Events are scaled to the
95% quantile of the population it has been assigned to. Barcodes with
less than 50 event assignments will be skipped; it is strongly recoomended
to remove such populations or reconsider their separation cutoffs.
Helena Lucia Crowell crowellh@student.ethz.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.
data(sample_ff, sample_key) # view preliminary assignments re <- assignPrelim(x = sample_ff, y = sample_key) plotEvents(x = re, which = "D1", n_events = 1000) # apply deconvolution parameters re <- estCutoffs(re) re <- applyCutoffs(x = re) plotEvents(x = re, which = "D1", n_events = 500)