plotEmbedding: Plot 2D embedding

In JEFworks/MERingue: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Plot 2D embedding

Description

Plot 2D embedding

Usage

plotEmbedding(
  emb,
  groups = NULL,
  colors = NULL,
  cex = 0.6,
  alpha = 0.4,
  gradientPalette = NULL,
  zlim = NULL,
  s = 1,
  v = 0.8,
  min.group.size = 1,
  show.legend = FALSE,
  mark.clusters = FALSE,
  mark.cluster.cex = 2,
  shuffle.colors = FALSE,
  legend.x = "topright",
  gradient.range.quantile = 0.95,
  verbose = FALSE,
  unclassified.cell.color = "lightgrey",
  group.level.colors = NULL,
  xlab = NA,
  ylab = NA,
  ...
)

Arguments

emb	dataframe with x and y coordinates
groups	factor annotations for rows on emb for visualizing cluster annotations
colors	color or numeric values for rows on emb for visualizing gene expression
cex	point size
alpha	point opacity
gradientPalette	palette for colors if numeric values provided
zlim	range for colors
s	saturation of rainbow for group colors
v	value of rainbow for group colors
min.group.size	minimum size of group in order for group to be colored
show.legend	whether to show legend
mark.clusters	whether to mark clusters with name of cluster
mark.cluster.cex	cluster marker point size
shuffle.colors	whether to shuffle group colors
legend.x	legend position ie. 'topright', 'topleft', 'bottomleft', 'bottomright'
gradient.range.quantile	quantile for mapping colors to gradient palette
verbose	verbosity
unclassified.cell.color	cells not included in groups will be labeled in this color
group.level.colors	set group level colors. Default uses rainbow.
xlab	x-axis label.
ylab	y-axis label.
...	Additional parameters to pass to BASE::plot

Value

None

Examples

data(mOB)
pos <- mOB$pos
gexp <- normalizeCounts(mOB$counts, log=FALSE, verbose=FALSE)['Camk4',]
plotEmbedding(pos, colors=scale(gexp)[,1], zlim=c(-2,2), cex=3)

JEFworks/MERingue documentation built on June 11, 2022, 4:16 a.m.