plotScatter | R Documentation |
Bivariate scatter plots including visualization of (group-specific) gates, their boundaries and percentage of selected cells.
plotScatter(
x,
chs,
color_by = NULL,
facet_by = NULL,
bins = 100,
assay = "exprs",
label = c("target", "channel", "both"),
zeros = FALSE,
k_pal = .cluster_cols
)
x |
a |
chs |
character string pecifying which channels to plot.
Valid values are antigens: |
color_by |
character string specifying
a cell metadata column to color by; valid values are
|
facet_by |
character string specifying a non-numeric
cell metadata column to facet by; valid values are
|
bins |
numeric of length 1 giving the number of bins
for |
assay |
character string specifying which assay data to use.
Should be one of |
label |
character string specifying axis labels should include antigen targets, channel names, or a concatenation of both. |
zeros |
logical specifying whether to include 0 values. |
k_pal |
character string specifying the cluster color palette;
ignored when |
a ggplot
object.
Helena L Crowell helena.crowell@uzh.ch
data(raw_data)
sce <- prepData(raw_data)
dna_chs <- c("DNA1", "DNA2")
plotScatter(sce, dna_chs, label = "both")
plotScatter(sce,
chs = sample(rownames(sce), 4),
color_by = "sample_id")
sce <- prepData(sample_ff)
ids <- sample(rownames(sample_key), 3)
sce <- assignPrelim(sce, sample_key[ids, ])
sce <- sce[, sce$bc_id %in% ids]
chs <- sample(rownames(sce), 5)
plotScatter(sce, chs, color_by = "bc_id")
plotScatter(sce, chs, color_by = "delta")
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