ssc.plot.violin: Plot violin

In Japrin/sscVis: simpler single cell RNAseq data Visualization

Plot violin

Description

Plot violin

Usage

ssc.plot.violin(
  obj,
  assay.name = "exprs",
  gene = NULL,
  columns = NULL,
  par.legend = list(),
  extra.var = NULL,
  group.var = "majorCluster",
  group.in = NULL,
  splitBy = NULL,
  clamp = c(0, 12),
  adjB = NULL,
  do.scale = F,
  angle.axis.x = 60,
  add = NULL,
  par.violin = list(scale = "width", color = NA, show.legend = T),
  par.boxplot = list(outlier.shape = NA, width = 0.25, alpha = 0.8),
  par.text = list(vjust = 0),
  par.pointrange = list(groupBy = NULL),
  palette.name = "YlOrRd",
  do.facet = T,
  out.prefix = NULL,
  p.ncol = 1,
  base_aspect_ratio = 1.1,
  ...
)

Arguments

obj	object of SingleCellExperiment class
assay.name	character; which assay (default: "exprs")
gene	character; genes to be showed. (default: NULL)
columns	character; columns in colData(obj) to be showd. (default: NULL)
par.legend	list; lengend parameters, used to overwrite the default setting; (default: list())
extra.var	character; extra column(s) in the colData(obj) to be kept. (default: NULL)
group.var	character; column in the colData(obj) used for grouping. (default: "majorCluster")
group.in	character; only thoes groups to be shown. NULL for all groups. (default: NULL)
splitBy	character; columns in colData(obj). Split the dataset to mupltiple subset then plot them one by one (default: NULL)
clamp	integer vector; expression values will be clamped to the range defined by this parameter. (default: c(0,12))
adjB	character; batch column of the colData(obj). (default: NULL)
do.scale	logical; whether scale the expression value. (default: FALSE)
angle.axis.x	numeric; rotation angle. (default 60)
add	character; other plots to add. one of "boxplot", "text", "" (default NULL)
par.violin	list; geom_violin parameters. (default: list(scale = "width",color=NA,show.legend = T))
par.boxplot	list; geom_boxplot parameters. (default: list(outlier.shape = NA,width=0.25,alpha=0.8))
par.text	list; geom_text parameters. (default: list(vjust=0))
par.pointrange	list; . (default: list(groupBy=NULL))
palette.name	character; which palette to use. (default: "YlOrRd")
do.facet	logical; facet the plot?. (default: TRUE)
out.prefix	character; output prefix. (default: NULL)
p.ncol	integer; number of columns in the figure layout. (default: 3)
base_aspect_ratio	numeric; base_aspect_ratio, used for plotting metadata. (default 1.1)
...	parameter passed to cowplot::save_plot

Details

If ‘gene' is not NULL, violin of the genes’ expression will be plot; if columns in not NULL, colData of obj with names in 'columns' will be plot in violin.

Japrin/sscVis documentation built on March 5, 2025, 10:23 a.m.