plotCTCompositionInNicheCluster — plotCTCompositionInNicheCluster • Giotto

plot cell type composition within each niche cluster

plotCTCompositionInNicheCluster(
  gobject,
  cell_type,
  values = "prob",
  spat_unit = "cell",
  feat_type = "niche cluster",
  normalization = c("by_niche_cluster", "by_cell_type", NULL),
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "CellTypeCompositionInNicheCluster"
)

Arguments

gobject: giotto object
cell_type: the cell type column name in the metadata
values: name of the expression matrix stored probability of each cell assigned to each niche cluster
spat_unit: name of spatial unit niche stored cluster features
feat_type: name of the feature type stored probability matrix
normalization: normalization method for the cell type composition
show_plot: logical. show plot
return_plot: logical. return ggplot object
save_plot: logical. save the plot
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

Value

ggplot

Details

This function plots the cell type composition within each niche cluster