Displays the pathway analysis results form running the 'FishersPathwayAnalysis()' function
Usage
VisualisePathways(
SpaMTP,
pathway_df,
assay = "SPM",
slot = "counts",
min_n = 3,
p_val_threshold = 0.1,
method = "ward.D2",
verbose = TRUE,
...
)Arguments
- SpaMTP
SpaMTP Seurat object used to run FishersPathwayAnalysis function.
- pathway_df
Dataframe containing the pathway enrichment results (output from SpaMTP::FishersPathwayAnalysis function).
- assay
Character string defining the SpaMTP assay that contains m/z values (default = "SPM").
- slot
Character string defining the assay slot contain the intensity values (default = "counts").
- min_n
Integer value specifying the minimum number of analytes required to be present in a pathway (default = 3).
- p_val_threshold
The p-val cutoff to keep the pathways generated from fisher exact test (default = "0.1").
- method
Character string defining the statistical method used to calculate hclust (default = "ward.D2").
- verbose
Boolean indicating whether to show informative messages. If FALSE these messages will be suppressed (default = TRUE).
- ...
The arguments pass to stats::hclust