plot_heatmap: plot_heatmap

In reactome/ReactomeGSA: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

plot_heatmap

Description

Creates a heatmap to show which pathways are up- and down-regulated in different datasets

Usage

plot_heatmap(
  x,
  fdr = 0.01,
  max_pathways = 30,
  break_long_names = TRUE,
  return_data = FALSE
)

Arguments

x	ReactomeAnalysisResult. The result object to use as input
fdr	numeric. The minimum FDR to consider a pathways as significantly regulated. (Default 0.01)
max_pathways	numeric. The maximum number of pathways to plot. Pathways are sorted based on in how many datasets they are significantly regulated. This has no effect if return_data is set to TRUE.
break_long_names	logical. If set, long pathway names are broken into two lines.
return_data	logical. If set, only the plotting data, but not the plot object itself is returned. This can be used to create customized plots that use the same data structure.

Value

A ggplot2 plot object representing the heatmap of pathways

See Also

Other ReactomeAnalysisResult functions: get_result(), names,ReactomeAnalysisResult-method, open_reactome(), pathways(), plot_correlations(), plot_gsva_heatmap(), plot_gsva_pathway(), plot_volcano(), reactome_links(), result_types()

Examples

# load an example result
library(ReactomeGSA.data)
data(griss_melanoma_result)

# create the heatmap plot
plot_obj <- plot_heatmap(griss_melanoma_result)

# show the plot
print(plot_obj)

reactome/ReactomeGSA documentation built on Nov. 13, 2023, 11:13 p.m.