heatmapPlot | R Documentation |
This function plot the significantly enriched terms in a heatmap by calling pheatmap package.
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,...)
enrichresult |
a list of data frames with enrichment results, alternatively output by |
GO |
logical to determine whether the terms are Gene Ontology(GO) terms enriched by |
terms |
a character vector to specify the terms chosen to be listed in the heatmap, selected from the |
padjust |
logical to determine whether the significantly enriched terms were selected by adjusted p.value
rather than the p.value, default to |
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 |
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 |
annotated_row |
logical to determine whether the the rows are annotated by |
display_numbers |
logical to determine whether the gene counts number is shown on the heatmap. |
heatmap plot and the terms with p.values for the heatmap
# 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)
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