Plot normalized counts for a gene

Plot for normalized counts of a single gene, with jittered points superimposed on the boxplot

ggplotCounts(
  dds,
  gene,
  intgroup = "condition",
  annotation_obj = NULL,
  transform = TRUE,
  labels_repel = TRUE
)

Arguments

dds

A DESeq2::DESeqDataSet() object.

gene

A character, specifying the name of the gene to plot

intgroup

Interesting groups: a character vector of names in colData(dds) to use for grouping

annotation_obj

A data.frame object, with row.names as gene identifiers (e.g. ENSEMBL ids) and a column, gene_name, containing e.g. HGNC-based gene symbols. Optional.

transform

Logical value, corresponding whether to have log scale y-axis or not. Defaults to TRUE.

labels_repel

Logical value. Whether to use ggrepel's functions to place labels; defaults to TRUE.

Value

An object created by ggplot

Details

Note: this function relies on the DESeq2::plotCounts() function of DESeq2, therefore pseudocounts of 0.5 are added to each point

Examples

library("airway")
data("airway", package = "airway")
airway
#> class: RangedSummarizedExperiment 
#> dim: 63677 8 
#> metadata(1): ''
#> assays(1): counts
#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
#>   ENSG00000273493
#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
#> colData names(9): SampleName cell ... Sample BioSample
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
  colData = colData(airway),
  design = ~ cell + dex
)
ggplotCounts(dds_airway,
  gene = "ENSG00000103196", # CRISPLD2 in the original publication
  intgroup = "dex"
)
#> Warning: Please use `mosdef::gene_plot()` in replacement of the `ggplotCounts()` function, originally located in the ideal package. 
#> Check the manual page for `?mosdef::gene_plot()` to see the details on how to use it, e.g. refer to the new parameter definition and naming