plotHeatmap: Plot Heatmap

In brianbennettphd/goSTAG: A tool to use GO Subtrees to Tag and Annotate Genes within a set

Description

Plots a heatmap of goSTAG analysis results.

Usage

plotHeatmap(enrichment_matrix, hclust_results, clusters, cluster_labels, sample_hclust_results = NULL, min_num_terms = 10, maximum_heatmap_value = 10, heatmap_colors = "auto", sample_colors = NULL, margin_size = 0.01, dendrogram_width = 0.4, cluster_label_width = 0.5, header_height = 0.3, sample_label_height = 0.6, dendrogram_lwd = 1, header_lwd = 1, cluster_label_cex = 1, sample_label_cex = 1)

Arguments

enrichment_matrix	A matrix of enrichment scores. Rows correspond to GO terms and columns correspond to gene lists.
hclust_results	An object of class "hclust" containing a tree produced by hierarchical clustering. This tree is for the GO terms (rows) in the enrichment matrix.
clusters	A list of vectors. Each element of the list corresponds to a cluster, and each vector contains the GO terms in the cluster.
cluster_labels	A vector of cluster labels.
sample_hclust_results	An object of class "hclust" containing a tree produced by hierarchical clustering. This tree is for the samples (columns) in the enrichment matrix. If NULL (default), the samples will appear in their original order with no dendrogram.
min_num_terms	The minimum number of GO terms required to plot a cluster label. Any cluster with fewer GO terms will not be labeled.
maximum_heatmap_value	The maximum value in the heatmap. Any values in the enrichment matrix greater than this value will be made equal to this value. This is to increase contrast in the heatmap by controlling outliers.
heatmap_colors	The color range for the heatmap. Available options are "auto", "extra", or a vector containing the color range. If "auto" (default), this function will use a color range from grey to red. If "extra", this function will use a color range from grey to yellow to red.
sample_colors	A vector of colors for the sample labels. If NULL (default), the sample labels will not have any color.
margin_size	The size of the margin between the elements of the plot, as a percentage of the entire width of the plot.
dendrogram_width	The size of the GO term dendrogram (including the cluster labels), as a percentage of the entire width of the plot (excluding the margins).
cluster_label_width	The size of the cluster labels, as a percentage of the GO term dendrogram.
header_height	The size of the header (including the sample labels), as a percentage of the entire height of the plot (excluding the margins).
sample_label_height	The size of the sample labels, as a percentage of the header.
dendrogram_lwd	The width of the GO term dendrogram lines.
header_lwd	The width of the sample dendrogram lines.
cluster_label_cex	A value that scales the cluster label text size.
sample_label_cex	A value that scales the sample label text size.

Value

None, the function is invoked for its side effect.

Author(s)

Brian D. Bennett
Pierre R. Bushel

References

Bennett BD and Bushel PR. goSTAG: Gene Ontology Subtrees to Tag and Annotate Genes within a set. Source Code Biol Med. 2017 Apr 13.

Examples

data( goSTAG_example_gene_lists )
go_terms <- loadGOTerms()
enrichment_matrix <- performGOEnrichment( goSTAG_example_gene_lists, go_terms )
hclust_results <- performHierarchicalClustering( enrichment_matrix )
clusters <- groupClusters( hclust_results )
cluster_labels <- annotateClusters( clusters )

plotHeatmap( enrichment_matrix, hclust_results, clusters, cluster_labels )

brianbennettphd/goSTAG documentation built on Nov. 14, 2020, 7:21 a.m.