plotGene: Plot Individual Genes

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Plot Individual Genes

Usage

## S4 method for signature 'SummarizedExperiment'
plotGene(object, genes, interestingGroups,
  countsAxisLabel = "counts", medianLine = TRUE,
  color = scale_color_hue(), headerLevel = 2L, return = c("facet", "wide",
  "grid", "markdown", "list"))

## S4 method for signature 'bcbioRNASeq'
plotGene(object, normalized = c("rlog", "vst", "tpm"),
  ...)

## S4 method for signature 'DESeqDataSet'
plotGene(object, ...)

## S4 method for signature 'DESeqTransform'
plotGene(object, ...)

Arguments

object	Object.
genes	Character vector of genes to include. These must match the rownames of the object. It is best practice to use the stable gene identifiers from Ensembl (e.g. "ENSG00000000003") and not the gene symbols.
interestingGroups	Character vector denoting groups of interest that define the samples. If left unset, defaults to sampleName.
countsAxisLabel	Label to use for the counts axis.
medianLine	Include median line for each group. Disabled if samples are colored by sample name.
color	Desired ggplot color scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
headerLevel	R Markdown header level.
return	Object class to return. Uses match.arg() internally and picks the first item in the vector by default.
normalized	Character indicating which normalization method to apply: "tpm": Transcripts per million (tximport). "tmm": edgeR trimmed mean of M-values. Calculated on the fly. "rlog": DESeq2 log2 regularized log transformation. "vst": DESeq2 log2 variance stabilizing transformation.
...	Additional arguments.

Value

• "grid": Show cowplot::plot_grid(), paneled per gene.

• "wide": Show ggplot in wide format, with genes on the x-axis.

• "list": list, containing per gene ggplot objects.

• "markdown": Show tabset R Markdown output, tabbed per gene.

Author(s)

Michael Steinbaugh

See Also

DESeq2::plotCounts().

Examples

# Gene identifiers
genes <- head(rownames(bcb_small), 8L)

# bcbioRNASeq ====
plotGene(bcb_small, genes = genes, return = "grid")
plotGene(bcb_small, genes = genes, return = "wide")

# DESeqDataSet ====
plotGene(dds_small, genes = genes)

# DESeqTransform ====
plotGene(rld_small, genes = genes)

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.