showProbPlot: Show distribution plots of the cell proportions generated by...

In SpatialDDLS: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Show distribution plots of the cell proportions generated by genMixedCellProp

Description

Show distribution plots of the cell proportions generated by the genMixedCellProp function.

Usage

showProbPlot(object, type.data, set, type.plot = "boxplot")

Arguments

object	SpatialDDLS object with prob.cell.types slot with plot slot.
type.data	Subset of data to show: train or test.
set	Integer determining which of the 6 different subsets to display.
type.plot	Character determining which type of visualization to display. It can be 'boxplot', 'violinplot', 'linesplot' or 'ncelltypes'. See Description for more information.

Details

These frequencies will determine the proportion of different cell types used during the simulation of mixed transcriptional profiles. Proportions generated by each method (see ?genMixedCellProp) can be visualized in three ways: box plots, violin plots, and lines plots. You can also plot the probabilities based on the number of different cell types present in the samples by setting type.plot = 'nCellTypes'.

Value

A ggplot object.

See Also

genMixedCellProp

Examples

set.seed(123)
sce <- SingleCellExperiment::SingleCellExperiment(
  assays = list(
    counts = matrix(
      rpois(100, lambda = 5), nrow = 40, ncol = 30,
      dimnames = list(paste0("Gene", seq(40)), paste0("RHC", seq(30)))
    )
  ),
  colData = data.frame(
    Cell_ID = paste0("RHC", seq(30)),
    Cell_Type = sample(x = paste0("CellType", seq(4)), size = 30,
                       replace = TRUE)
  ),
  rowData = data.frame(
    Gene_ID = paste0("Gene", seq(40))
  )
)

SDDLS <- createSpatialDDLSobject(
  sc.data = sce,
  sc.cell.ID.column = "Cell_ID",
  sc.gene.ID.column = "Gene_ID",
  project = "Simul_example",
  sc.filt.genes.cluster = FALSE
)
SDDLS <- genMixedCellProp(
  object = SDDLS,
  cell.ID.column = "Cell_ID",
  cell.type.column = "Cell_Type",
  num.sim.spots = 10, 
  train.freq.cells = 2/3,
  train.freq.spots = 2/3,
  verbose = TRUE
)
showProbPlot(
   SDDLS,
   type.data = "train",
   set = 1,
   type.plot = "boxplot"
 )
 

SpatialDDLS documentation built on Oct. 31, 2024, 5:07 p.m.