plotsymbolsmap: Plotting groups as different symbols in a dimensional reduction representation

Description

This functions highlights groups of cells by different symbols in a two-dimensional t-SNE map, UMAP, or a Fruchterman-Rheingold graph layout of the singe-cell transcriptome data.

Usage

plotsymbolsmap(
  object,
  types,
  subset = NULL,
  samples_col = NULL,
  cex = 0.5,
  fr = FALSE,
  um = FALSE,
  leg = TRUE,
  map = TRUE,
  cex.legend = 0.75,
  leg.pos = "topleft"
)

Value

None

Arguments

object: SCseq class object.
types: Vector assigning each cell to a type to be highlighted in the t-SNE map. The order has to be the same as for the columns in slot ndata of the SCseq object. Default is NULL and each cell is highlighted by a different symbol.
subset: Vector containing a subset of types from types to be highlighted in the map. Default is NULL and all types are shown.
samples_col: Vector of colors used for highlighting all samples contained in samples in the map. Default is NULL.
cex: size of data points. Default value is 0.5.
fr: logical. If TRUE then plot Fruchterman-Rheingold layout. Default is FALSE.
um: logical. If TRUE then plot umap dimensional reduction representation. Default is FALSE.
leg: logical. If TRUE then the legend is shown. Default value is TRUE.
map: logical. If TRUE then data points are shown. Default value is TRUE.
cex.legend: Positive real number. Size of data points and text in the legend. Default is 0.75.
leg.pos: Position of the legend. a single keyword from the list ‘"bottomright"’, ‘"bottom"’, ‘"bottomleft"’,‘"left"’, ‘"topleft"’, ‘"top"’, ‘"topright"’, ‘"right"’ and‘"center"’. This places the legend on the inside of the plot frame at the given location.