plotScatter: Scatter plot

In CATALYST: Cytometry dATa anALYSis Tools

Description

Bivariate scatter plots including visualization of (group-specific) gates, their boundaries and percentage of selected cells.

Usage

plotScatter(
  x,
  chs,
  color_by = NULL,
  facet_by = NULL,
  bins = 100,
  assay = "exprs",
  label = c("target", "channel", "both"),
  zeros = FALSE,
  k_pal = CATALYST:::.cluster_cols
)

Arguments

x	a SingleCellExperiment.
chs	character string pecifying which channels to plot. Valid values are antigens: rownames(x), channel names: channels(x) or non-mass channels stored in names([int_]colData(x)), and should correspond to numeric variables.
color_by	character string specifying a cell metadata column to color by; valid values are names(colData(x)), names(int_colData(x)); names(cluster_codes(x)) (if cluster has been run); or NULL to color by density.
facet_by	character string specifying a non-numeric cell metadata column to facet by; valid values are names(colData(x)). When length(chs) == 1, 2 facetting variables may be provided, otherwise 1 only.
bins	numeric of length 1 giving the number of bins for geom_hex when coloring by density.
assay	character string specifying which assay data to use. Should be one of assayNames(x).
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 color_by is not one of names(cluster_codes(x)). If less than nlevels(cluster_ids(x, k)) are supplied, colors will be interpolated via colorRampPalette.

Value

a ggplot object.

Author(s)

Helena L Crowell [e-mail]

Examples

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")

CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.