ggplotCounts {ideal} | R Documentation

## Plot normalized counts for a gene

### Description

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

### Usage

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

### Arguments

`dds` | A `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.

### Details

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

### Value

An object created by `ggplot`

### Examples

    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                                 colData = colData(airway),
                                                 design=~cell+dex)
    ggplotCounts(dds_airway,
                 gene = "ENSG00000103196", # CRISPLD2 in the original publication
                 intgroup = "dex")

[Package ideal version 1.11.2 Index]