plotCorrelationHeatmap: Plot Correlation Heatmap

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

This function calculates a correlation matrix based on feature expression per sample.

Usage

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

Arguments

object	Object.
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.
...	Passthrough arguments to SummarizedExperiment method.

Value

Show heatmap and invisibly return a list of the components.

Author(s)

Michael Steinbaugh

See Also

• help("plotCorrelationHeatmap", "bcbioBase").

• findMethod("plotCorrelationHeatmap", "SummarizedExperiment").

Other Quality Control Functions: plot5Prime3PrimeBias, plotCountDensity, plotCountsPerGene, plotDispEsts, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotMeanSD, plotPCACovariates, plotPCA, plotRRNAMappingRate, plotTotalReads

Examples

# bcbioRNASeq ====
# Pearson correlation
plotCorrelationHeatmap(bcb_small, method = "pearson")

# Spearman correlation
plotCorrelationHeatmap(bcb_small, method = "spearman")

# Inferno palette
plotCorrelationHeatmap(
    bcb_small,
    color = inferno,
    legendColor = inferno
)

# Default pheatmap palette
plotCorrelationHeatmap(
    bcb_small,
    color = NULL,
    legendColor = NULL
)

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