Plot dimensional reduction

Displays the dimensional reduction and maps gene, gene-set or feature information onto the color-aesthetic.

plotUMAP(
  object,
  of_sample = "",
  color_to = NULL,
  method_gs = "mean",
  pt_size = 2,
  pt_alpha = 1,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  verbose = TRUE
)

plotTSNE(
  object,
  of_sample = "",
  color_to = NULL,
  method_gs = "mean",
  pt_size = 2,
  pt_alpha = 1,
  pt_clrsp = "inferno",
  pt_clrp = "milo",
  verbose = TRUE
)

Arguments

object	A valid spata-object.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
color_to	The variable to be displayed by color: Gene set as a single character value. Must be in getGeneSets() Genes as a character vector. If more than one gene is specified the average expression of those genes will be calculated and displayed. Must be in getGenes() Feature as a single character value. Must be in getFeaturenNames()
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean' or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA().
pt_size	The size of the points specified as a single numeric value.
pt_alpha	The transparency of the points specified as single numeric value.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run all_colorspectra() to see valid input..
pt_clrp	The color panel to be used if the specified variable displayed by color is categorical/discrete. Run all_colorpanels() to see valid input.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.