ssc.plot.tsne: Plot on tSNE map

In Japrin/sscVis: simpler single cell RNAseq data Visualization

Plot on tSNE map

Description

Plot on tSNE map

Usage

ssc.plot.tsne(
  obj,
  assay.name = "exprs",
  gene = NULL,
  columns = NULL,
  splitBy = NULL,
  plotDensity = F,
  colSet = list(),
  reduced.name = "iCor.tsne",
  reduced.dim = c(1, 2),
  xlim = NULL,
  ylim = NULL,
  size = NULL,
  palette.name = "YlOrRd",
  adjB = NULL,
  clamp = "none",
  do.scale = FALSE,
  label = NULL,
  par.repel = list(force = 1),
  my.ggPoint = geom_point,
  par.geom_point = list(),
  par.legend = list(),
  show.legend = NULL,
  theme.use = theme_bw,
  legend.w = 1,
  verbose = F,
  fun.extra = NULL,
  par.geneOnTSNE = list(scales = "free", pt.order = "value", pt.alpha = 0.1),
  out.prefix = NULL,
  p.ncol = 3,
  width = NA,
  height = NA,
  base_aspect_ratio = 1.1,
  peaks = NULL
)

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)
splitBy	character; columns in colData(obj). Split the dataset to mupltiple subset then plot them one by one (default: NULL)
plotDensity	logical; whether plot 2D density. (default F)
colSet	list; mapping iterms in the names to colors in the values. (default: list())
reduced.name	character; names in the reducedDimNames. (default: "iCor.tsne")
reduced.dim	integer; which dimensions of the reduced data to be used. (default: c(1,2))
xlim	integer or NULL; only draw points lie in the ragne specified by xlim and ylim (default NULL)
ylim	integer or NULL; only draw points lie in the ragne specified by xlim and ylim (default NULL)
size	double; points' size. If NULL, infer from number of points (default NULL)
palette.name	character; which palette to use. (default: "YlOrRd")
adjB	character; batch column of the colData(obj). (default: NULL)
clamp	integer vector; expression values will be clamped to the range defined by this parameter, such as c(0,15). (default: "none" )
do.scale	logical; whether scale the expression value. (default: FALSE)
label	double; label size. if NULL, no label showed. (default: NULL )
par.repel	list; passed to geom_text_repel
my.ggPoint	function; used to plot scatter plot, such as geom_point, geom_point_rast, geom_scattermore, geom_scattermost (default: geom_point)
par.geom_point	list; extra parameters for geom_point/geom_point_rast; (default: list())
par.legend	list; lengend parameters, used to overwrite the default setting; (default: list())
show.legend	logical; if NULL, determined automatically; (default: NULL)
theme.use	function; which theme to use (default: theme_bw)
legend.w	numeric; adjust legend width (default: 1)
verbose	logical; (default: FALSE)
fun.extra	function; (default: NULL)
par.geneOnTSNE	character; other parameters of geneOnTSNE
out.prefix	character; output prefix. (default: NULL)
p.ncol	integer; number of columns in the figure layout. (default: 3)
width	numeric; width of the plot, used for geneOnTSNE. (default: NA)
height	numeric; height of the plot, used for geneOnTSNE. (default: NA)
base_aspect_ratio	numeric; base_aspect_ratio, used for plotting metadata. (default 1.1)
peaks	integer or character; index or names of the peaks. (default: NULL)

Details

If 'gene' is not NULL, expression of the specified genes will be plot on the tSNE map; if columns in not NULL, colData of obj with names in 'columns' will be plot on the tSNE map. The tSNE map used is specified by option 'reduced.name' and 'reduced.dim'. Both 'gene' and 'columns' can be non-NULL. For list 'colSet', each element define a color mapping for the responding iterm in the 'column'; if not specifed, automatically generated color mapping will be used.

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