cellProximityHeatmap

Create heatmap from cell-cell proximity scores

cellProximityHeatmap(
  gobject,
  CPscore,
  scale = TRUE,
  order_cell_types = TRUE,
  color_breaks = NULL,
  color_names = NULL,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "cellProximityHeatmap"
)

Arguments

gobject

giotto object

CPscore

CPscore, output from cellProximityEnrichment()

scale

scale cell-cell proximity interaction scores

order_cell_types

order cell types based on enrichment correlation

color_breaks

numerical vector of length 3 to represent min, mean and maximum

color_names

character color vector of length 3

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 heatmap

Details

This function creates a heatmap that shows the spatial proximity enrichment or depletion of cell type pairs.

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> cell_spatInfo_spatVector.shp
#> cell
#> 
#> 3.2 read Giotto spatial centroid information
#> cell
#> 
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#>  skipped
#> 
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#>  "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"

x <- cellProximityEnrichment(g, cluster_column = "leiden_clus")

cellProximityHeatmap(gobject = g, CPscore = x)