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...
#> 0.054 secs
#>   CD14+ Monocytes...
#> 0.087 secs
#>   CD4 T cells...
#> 0.065 secs
#>   CD8 T cells...
#> 0.039 secs
#>   FCGR3A+ Monocytes...
#> 0.092 secs

# Differential expression analysis within each assay,
# evaluated on the voom normalized data
res.dl <- dreamlet(res.proc, ~group_id)
#>   B cells...
#> 0.049 secs
#>   CD14+ Monocytes...
#> 0.064 secs
#>   CD4 T cells...
#> 0.052 secs
#>   CD8 T cells...
#> 0.034 secs
#>   FCGR3A+ Monocytes...
#> 0.063 secs

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