Sort variance partition statistics

Usage

# S4 method for class 'vpDF'
sortCols(
  x,
  FUN = sum,
  decreasing = TRUE,
  last = c("Residuals", "Measurement.error"),
  ...
)

Arguments

x: object returned by fitVarPart()
FUN: function giving summary statistic to sort by. Defaults to sum
decreasing: logical. Should the sorting be increasing or decreasing?
last: columns to be placed on the right, regardless of values in these columns
...: other arguments to sort

Value

data.frame with columns sorted by mean value, with Residuals in last column

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

# create pseudobulk for each sample and cell cluster
pb <- aggregateToPseudoBulk(example_sce,
  assay = "counts",
  cluster_id = "cluster_id",
  sample_id = "sample_id",
  verbose = FALSE
)

# voom-style normalization
res.proc <- processAssays(pb, ~group_id)
#>   B cells...
#> 0.053 secs
#>   CD14+ Monocytes...
#> 0.085 secs
#>   CD4 T cells...
#> 0.062 secs
#>   CD8 T cells...
#> 0.045 secs
#>   FCGR3A+ Monocytes...
#> 0.079 secs

# variance partitioning analysis
vp <- fitVarPart(res.proc, ~group_id)
#>   B cells...
#> 0.59 secs
#>   CD14+ Monocytes...
#> 0.78 secs
#>   CD4 T cells...
#> 0.62 secs
#>   CD8 T cells...
#> 0.38 secs
#>   FCGR3A+ Monocytes...
#> 0.75 secs
#> 

# Summarize variance fractions genome-wide for each cell type
plotVarPart(sortCols(vp))