plotRLExpr: Compute and plot relative log expression (RLE) values of gene...

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Compute and plot relative log expression (RLE) values of gene expression data

Description

Compute and plot relative log expression (RLE) values of gene expression data

Usage

plotRLExpr(object, ordannots = c(), ...)

## S4 method for signature 'DGEList'
plotRLExpr(object, ordannots = c(), ...)

## S4 method for signature 'ExpressionSet'
plotRLExpr(object, ordannots = c(), ...)

## S4 method for signature 'SummarizedExperiment'
plotRLExpr(object, ordannots, assay = 1, sce_thresh = 1000, ...)

Arguments

object	a DGEList, SummarizedExperiment or ExpressionSet object containing gene expression data.
ordannots	variables or computations to sort samples by (tidy style).
...	aesthetic mappings to pass to ggplot2::aes_string().
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment and its derivative classes).
sce_thresh	Integer value. The threshold of sample size for using dot plot instead of box plot.

Value

a ggplot2 object, containing the RLE plot.

Examples

data("dkd_spe_subset")
plotRLExpr(dkd_spe_subset)

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.