Beeswarm plot of effect sizes for each assay

Beeswarm plot of effect sizes for each assay, colored by sign and FDR

Usage

plotBeeswarm(res.dl, coef, fdr.range = 4, assays = assayNames(res.dl))

Arguments

res.dl

dreamletResult object from dreamlet()

coef

coefficient name fed to topTable()

fdr.range

range for coloring FDR

assays

which assays to plot

Value

ggplot2 of logFC by assay

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...
#> 0.13 secs
#>   CD14+ Monocytes...
#> 0.23 secs
#>   CD4 T cells...
#> 0.16 secs
#>   CD8 T cells...
#> 0.077 secs
#>   FCGR3A+ Monocytes...
#> 0.2 secs

# Differential expression analysis within each assay,
# evaluated on the voom normalized data
res.dl <- dreamlet(res.proc, ~group_id)
#>   B cells...
#> 0.091 secs
#>   CD14+ Monocytes...
#> 0.12 secs
#>   CD4 T cells...
#> 0.1 secs
#>   CD8 T cells...
#> 0.056 secs
#>   FCGR3A+ Monocytes...
#> 0.12 secs

# Beeswarm plot of effect sizes for each assay,
# colored by sign and FDR
plotBeeswarm(res.dl, "group_idstim")