plotMeanAverage: Plot Mean Average

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Plot Mean Average

Usage

plotMeanAverage(object, ...)

## S4 method for signature 'DESeqResults'
plotMeanAverage(object, alpha, lfcThreshold = 0L,
  genes = NULL, gene2symbol = NULL, ntop = 0L, direction = c("both",
  "up", "down"), pointColor = "gray50", sigPointColor = c(upregulated =
  "purple", downregulated = "orange"), return = c("ggplot", "data.frame"))

Arguments

object	Object.
...	Additional arguments.
alpha	Adjusted P value ("alpha") cutoff.
lfcThreshold	Log fold change ratio (base 2) cutoff threshold.
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.
gene2symbol	data.frame containing gene-to-symbol mappings. Must contain the columns geneID and geneName.
ntop	Number of top genes to label.
direction	Plot "both", "up", or "down" directions.
pointColor	Default point color for the plot.
sigPointColor	character vector containing color names for labeling upregulated and downregulated genes. Also supports a character string for labeling DEGs with the same color, regardless of direction.
return	Object class to return. Uses match.arg() internally and picks the first item in the vector by default.

Value

ggplot.

Author(s)

Rory Kirchner, Michael Steinbaugh

See Also

DESeq2::plotMA().

Other Differential Expression Functions: alphaSummary, contrastName, plotDEGHeatmap, plotDEGPCA, plotVolcano, resultsTables

Examples

gene2symbol <- gene2symbol(bcb_small)

# DESeqResults ====
# Color DEGs in each direction separately
plotMeanAverage(
    object = res_small,
    sigPointColor = c(
        upregulated = "purple",
        downregulated = "orange"
    )
)

# Label DEGs with a single color
plotMeanAverage(res_small, sigPointColor = "purple")

# Directional support
plotMeanAverage(
    object = res_small,
    direction = "up",
    ntop = 5L,
    gene2symbol = gene2symbol
)
plotMeanAverage(
    object = res_small,
    direction = "down",
    ntop = 5L,
    gene2symbol = gene2symbol
)

# Label genes manually
plotMeanAverage(
    object = res_small,
    genes = head(rownames(res_small)),
    gene2symbol = gene2symbol
)

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