plot_gsva_heatmap,ReactomeAnalysisResult-method {ReactomeGSA} | R Documentation |
Plots pathway expression values / sample as a heatmap. Ranks pathways based on their expression difference.
## S4 method for signature 'ReactomeAnalysisResult' 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 the heatmap.2 function. |
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