createDiagnosticPlots: Create diagnostic Plots

In Sage-Bionetworks/SageBionetworksCoex: Gene Coexpression

Description

Given the output of Coexpression analysis, this creates a set of diagnostic plots (heatmaps and dendrograms), each in a file.

Usage

createDiagnosticPlots(filetype = "jpg", outputDir = NULL, expressionData, dichotCor, tomDist, connectivity, beta, geneTree, geneModules, genePCTree)

Arguments

filetype	One of "jpg", "pdf", "png", "ps", not case sensitive.
outputDir	The directory/folder into which the plots are to be written. If NULL, the session temporary directory is used.
expressionData	The input data for the analysis, a normalized matrix of gene expression data, given as a data frame with rows as samples and columns as genes/probes.
dichotCor	|cc|^beta, returned by clusterGenes()
tomDist	Topological Overlap Matrix (TOM) expressed as a distance matrix, returned by clusterGenes()
connectivity	The connectivity value (k) for each gene, as returned by clusterGenes()
beta	The scale-free exponent, returned by clusterGenes()
geneTree	The gene dendrogram, returned by clusterGenes()
geneModules	The module membership of each gene, returned by modulesFromGeneTree()
genePCTree	The dendrogram of module 'principal components', returned by modulesFromGeneTree()

Value

The file handles for the created plots.

ScaleFree	File handle to "Scale free" plot (P(k) vs. k) for optimum value of beta
CorHeatmap	File handle to heatmap of |cc|^beta, ordered according to dendrogram, with color-coded module membership along the margins
GeneDendrogram	File handle to gene dendrogram with color-coded modules and color names
TOMHeatmap	File handle to heatmap of TOM, rows and columns sorted by gene dendrogram
GenePCDendrogram	File handle to dendrogram of clusters of module representative genes
ExpressionHeatmap	File handle to heatmap of expression data, organized by gene and sample clusters

Note

TOM and Correlation heat maps are not generated correctly in Windows, though they are in Unix.

Author(s)

Bruce Hoff

References

Zhang, B. & Horvath, S. (2005) Statistical Applications in Genetics and Molecular Biology 4, Article 17.

Sage-Bionetworks/SageBionetworksCoex documentation built on May 9, 2019, 12:11 p.m.