plotCounts: Plot cell counts

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Plot cell counts

Description

Barplot of the number of cells measured for each sample.

Usage

plotCounts(x, group_by = "condition", color_by = group_by, prop = FALSE)

Arguments

x	a SingleCellExperiment.
group_by	character string specifying a non-numeric cell metadata column to group by (determines x-axis ticks); valid values are names(colData(x)).
color_by	character string specifying a non-numeric cell metadata column to color by (determines grouping of bars); valid values are names(colData(x)); NULL for no color.
prop	logical specifying whether to plot relative abundances (frequencies) for each group rather than total cell counts; bars will be stacked when prop = TRUE and dodged otherwise.

Value

a ggplot object.

Author(s)

Helena L Crowell [e-mail]

References

Nowicka M, Krieg C, Crowell HL, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

Examples

data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)

# plot number of cells per sample, colored by condition
plotCounts(sce, 
  group_by = "sample_id", 
  color_by = "condition")
  
# same as above, but order by patient  
plotCounts(sce, 
  group_by = "patient_id", 
  color_by = "condition")

# total number of cell per patient
plotCounts(sce, 
  group_by = "patient_id", 
  color_by = NULL)

# plot proportion of cells from each patient by condition
plotCounts(sce, 
  prop = TRUE, 
  group_by = "condition", 
  color_by = "patient_id")

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.