plotsymbolsmap: Plotting groups as different symbols in a dimensional...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

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"
)

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.

Value

None

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.