plotCellTypesFromEnrichment

plotCellTypesFromEnrichment(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  enrichment_name = "PAGE_z_score",
  title = NULL,
  save_param = list(),
  default_save_name = "cell_types_from_enrichment",
  save_plot = NULL,
  show_plot = NULL,
  return_plot = NULL
)

Arguments

gobject: Giotto Object
spat_unit: spatial unit in which the enrichment information is stored
feat_type: feature type for which the enrichment information was calculated
enrichment_name: name of the spatial enrichment i.e. output from GiottoClass::list_spatial_enrichment_names() Default value is "PAGE_Z_score"
title: Title of the generated plot. Default `paste0(spat_unit,"cell types (maximum", enrichment_name, ")")`
save_param: list of saving parameters, see showSaveParameters
default_save_name: default save name for saving, don't change, change save_name in save_param
save_plot: logical. save the plot
show_plot: logical. show plot
return_plot: logical. return ggplot object

Value

plot

Details

This function generates a bar plot of cell types vs the frequency of that cell type in the data. These cell type results are based on the provided `enrichment_name`, and will be determined by the maximum value of the z-score or p-value for a given cell or annotation.