showProbPlot | R Documentation |
generateBulkCellMatrix
Show distribution plots of the cell proportions generated by
generateBulkCellMatrix
. These frequencies will determine the
proportion of different cell types used during the simulation of pseudo-bulk
RNA-Seq samples. There are 6 subsets of proportions generated by different
approaches that 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'
.
showProbPlot(object, type.data, set, type.plot = "boxplot")
object |
|
type.data |
Subset of data to show: |
set |
Integer determining which of the 6 different subsets to display. |
type.plot |
Character determining which type of visualization to
display. It can be |
These plots are only for diagnostic purposes. This is the reason because they are generated without any parameter introduced by the user.
A ggplot object.
generateBulkCellMatrix
# simulating data set.seed(123) # reproducibility 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)) ) ) DDLS <- loadSCProfiles( single.cell.data = sce, cell.ID.column = "Cell_ID", gene.ID.column = "Gene_ID" ) probMatrix <- data.frame( Cell_Type = paste0("CellType", seq(4)), from = c(1, 1, 1, 30), to = c(15, 15, 50, 70) ) DDLS <- generateBulkCellMatrix( object = DDLS, cell.ID.column = "Cell_ID", cell.type.column = "Cell_Type", prob.design = probMatrix, num.bulk.samples = 60 ) lapply( X = 1:6, FUN = function(x) { showProbPlot( DDLS, type.data = "train", set = x, type.plot = "boxplot" ) } )
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