Plot probability distribution

Usage

plotProbDist(object, ...)

# S4 method for class 'matrix'
plotProbDist(object, targetCells = NA, ...)

# S4 method for class 'SpatialExperiment'
plotProbDist(
  object,
  pm_cols,
  targetCells = NA,
  by_cluster = FALSE,
  show_clusters = as.character(seq(6)),
  plot_all = FALSE,
  sample_size = 2,
  val_name = "clusters",
  ...
)

Arguments

object: A probability matrix or SpatialExperiment.
...: aesthetic mappings to pass to ggplot2::aes_string().
targetCells: Character. Optional. Can speicify one or more cells to be plotted.
pm_cols: The colnames of probability matrix. This is requires for SpatialExperiment input. Assuming that the probability is stored in the colData.
by_cluster: Logical. By default is TRUE, to plot distribution by each cluster.
show_clusters: Character. The cluster to be ploted, by default is 1 to 6.
plot_all: Logical. By default is FALSE, set this to true to plot box plot instead of bar plot to show all cells in each cluster.
sample_size: Integer. By default is 2, sampling two cell from each cluster to be plotted.
val_name: Character. Column name used to store the clusters.

Value

A ggplot object.

Examples


data("spe_test")

spe <- readHoodData(spe, anno_col = "celltypes")

fnc <- findNearCells(spe, k = 100)

pm <- scanHoods(fnc$distance)
#> Tau is set to: 22747.4

pm2 <- mergeByGroup(pm, fnc$cells)

spe <- mergeHoodSpe(spe, pm2)

plotProbDist(spe, pm_cols = colnames(pm2))