Plot probability matrix as a heatmap

Plot probability matrix as a heatmap

Usage

plotHoodMat(object, ...)

# S4 method for class 'matrix'
plotHoodMat(
  object,
  targetCells = NA,
  n = 30,
  hm_width = 4,
  hm_height = 15,
  clusterRows = TRUE,
  clusterCols = TRUE,
  title = "Probability of neighborhoods"
)

# S4 method for class 'SpatialExperiment'
plotHoodMat(
  object,
  pm_cols,
  targetCells = NA,
  n = 30,
  hm_width = 4,
  hm_height = 15,
  clusterRows = TRUE,
  clusterCols = TRUE,
  title = "Probability of neighborhoods"
)

Arguments

object

A probability matrix or SpatialExperiment.

...

Ignore parameter.

targetCells

Character. Optional. Can speicify one or more cells to be plotted.

n

Integer. The number of randomly selected cells to be plotted. This parameter will be used when targetCells is not specify.

hm_width

Integer. The width of heatmap.

hm_height

Integer. The height of heatmap.

clusterRows

Logical. Cluster rows or not.

clusterCols

Logical. Cluster columns or not.

title

Title of the heatmap.

pm_cols

The colnames of probability matrix. This is requires for SpatialExperiment input. Assuming that the probability is stored in the colData.

Value

A ComplexHeatmap plot.

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)

plotHoodMat(spe, pm_cols = colnames(pm2))