heatmapPlot {eegc} | R Documentation

## Heatmap Plot of Enriched Terms

### Description

This function plot the significantly enriched terms in a heatmap by calling pheatmap package.

### Usage

    heatmapPlot(enrichresult, GO = FALSE, terms = NULL, padjust = TRUE, pvalue = 0.05,
    top= NA, filter = FALSE, main = NA, annotation = NULL, annotation_col = NULL,
    annotated_row = FALSE, annotation_row = NULL,annotation_colors = NA,
    display_numbers = FALSE, annotation_legend = FALSE,...)

### Arguments

`enrichresult` | a list of data frames with enrichment results, alternatively output by `functionEnrich` or `enrichment`.
`GO` | logical to determine whether the terms are Gene Ontology(GO) terms enriched by `functionEnrich`.
`terms` | a character vector to specify the terms chosen to be listed in the heatmap, selected from the `enrichment` result, or a data frame with terms and corresponding term annotations used for `annotation_row`.
`padjust` | logical to determine whether the significantly enriched terms were selected by adjusted p.value rather than the p.value, default to `TRUE`.
`pvalue` | a cutoff value to select the significantly enriched terms.
`top` | a number to specify the most significantly enriched terms to be drawn in each category, default to `NA` without specifying.
`filter` | logical to specify whether the enriched terms need to be filered with the ones which are significant among the first four categories.
`main` | a character of main title on the heatmap plot.
`annotation, annotation_row, annotation_col, annotation_colors, annotation_legend, ...` | see details in `pheatmap`.
`annotated_row` | logical to determine whether the the rows are annotated by `annotation_row`, default to `FALSE`. When it's `TRUE`, `annotation_row` should be specified or using annotations in a data frame of `terms`.
`display_numbers` | logical to determine whether the gene counts number is shown on the heatmap.

### Value

heatmap plot and the terms with p.values for the heatmap

### Examples

    # plot the enrichment results by the five gene categories
    data(goenrich)
    heatmaptable = heatmapPlot(goenrich, GO = TRUE, top = 5, filter = FALSE,
                               main = "Gene ontology enrichment",
                               display_numbers =  FALSE)

[Package eegc version 1.6.1 Index]