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,
database = NULL,
database_version = "latest",
database_source = c("auto", "bundled", "local"),
database_local_dir = NULL,
...
)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).
- database
Optional named list of database resources, normally created by
LoadSpaMTPDatabase().- database_version
Database snapshot version used for pathway lookup.
- database_source
Database source; see
LoadSpaMTPDatabase().- database_local_dir
Optional local RDS resource directory.
- ...
The arguments pass to stats::hclust
Examples
utils::str(formals(VisualisePathways))
#> Dotted pair list of 13
#> $ SpaMTP : symbol
#> $ pathway_df : symbol
#> $ assay : chr "SPM"
#> $ slot : chr "counts"
#> $ min_n : num 3
#> $ p_val_threshold : num 0.1
#> $ method : chr "ward.D2"
#> $ verbose : logi TRUE
#> $ database : NULL
#> $ database_version : chr "latest"
#> $ database_source : language c("auto", "bundled", "local")
#> $ database_local_dir: NULL
#> $ ... : symbol
#SpaMTP:::VisualisePathways(SpaMTP =seurat,pathway_df = pathway_df,p_val_threshold = 0.1,assay = "Spatial",slot = "counts")