| plot_gsva_heatmap {ReactomeGSA} | R Documentation |
Plots pathway expression values / sample as a heatmap. Ranks pathways based on their expression difference.
plot_gsva_heatmap(object, pathway_ids = NULL, max_pathways = 20, truncate_names = TRUE, ...)
object |
The |
pathway_ids |
A vector of pathway ids. If set, only these pathways are included in the plot. |
max_pathways |
The maximum number of pathways to include. Only takes effect if |
truncate_names |
If set, long pathway names are truncated. |
... |
Additional parameters passed to specific implementations. |
None
Other ReactomeAnalysisResult functions: get_result,
names,ReactomeAnalysisResult-method,
open_reactome, pathways,
plot_correlations,
plot_gsva_pathway,
plot_volcano, reactome_links,
result_types
# load the scRNA-seq example data
library(ReactomeGSA.data)
data(jerby_b_cells)
# perform the GSVA analysis
gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE)
# plot the heatmap
relevant_pathways <- c("R-HSA-983170", "R-HSA-388841", "R-HSA-2132295", "R-HSA-983705", "R-HSA-5690714")
plot_gsva_heatmap(gsva_result,
pathway_ids = relevant_pathways, # limit to these pathways
margins = c(6,30), # adapt the figure margins in heatmap.2
dendrogram = "col", # only plot column dendrogram
scale = "row", # scale for each pathway
key = FALSE, # don't display the color key
lwid=c(0.1,4)) # remove the white space on the left