plotHeatmap: Heatmap

Description Usage Arguments Value Scaling Hierarchical clustering Note Author(s) See Also Examples

Description

Construct a simple heatmap.

Usage

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plotHeatmap(object, ...)

plotCorrelationHeatmap(object, ...)

plotQuantileHeatmap(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotHeatmap(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotCorrelationHeatmap(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotQuantileHeatmap(object, ...)

Arguments

object

Object.

...

Additional arguments.

Value

pheatmap.

Scaling

Here we're scaling simply by calculating the standard score (z-score).

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z = (x - mu) / sigma

See also:

Hierarchical clustering

Row- and column-wise hierarchical clustering is performed when clusterRows and/or clusterCols are set to TRUE. Internally, this calls hclust(), and defaults to the Ward method.

Automatic hierarchical clustering of rows and/or columns can error for some datasets. When this occurs, you'll likely see this error:

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Error in hclust(d, method = method) :
NA/NaN/Inf in foreign function call

In this case, either set clusterRows and/or clusterCols to FALSE, or you can attempt to pass an hclust object to these arguments. This is recommended as an alternate approach to be used with pheatmap(), which is called internally by our plotting code. Here's how this can be accomplished:

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mat <- assay(mat)
dist <- dist(mat)
hclust <- hclust(dist, method = "ward.D2")

Note

Updated 2020-08-04.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

Examples

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steinbaugh/DESeqAnalysis documentation built on Oct. 15, 2020, 2:02 a.m.