MetabolicPathwayHeterogeneity

Calculate Metabolic Pathway heterogeneity.

For each subset, the normalized enrichment score (NES) of each metabolic pathway is calculated for each group.
The NES is calculated by comparing the enrichment score of the subset to the enrichment scores of the same subset in the permutations.
The p-value is calculated by comparing the NES to the NESs of the same subset in the permutations.
The heterogeneity can be reflected by the NES values and the p-values in different groups for the metabolic pathways.

MetabolicPathwayHeterogeneity

Input

  • sobjfile:

Output

  • outdir: Default: {{in.sobjfile | stem}}.pathwayhetero.

Environment Variables

  • gmtfile (pgarg): The GMT file with the metabolic pathways.
    Defaults to ScrnaMetabolicLandscape.gmtfile
  • select_pcs (type=float): Default: 0.8.
    Select the PCs to use for the analysis.
  • pathway_pval_cutoff (type=float): Default: 0.01.
    The p-value cutoff to select the enriched pathways
  • ncores (type=int;pgarg): Default: 1.
    Number of cores to use for parallelization Defaults to ScrnaMetabolicLandscape.ncores
  • bubble_devpars (ns): The devpars for the bubble plot
    • width (type=int): The width of the plot
    • height (type=int): The height of the plot
    • res (type=int): The resolution of the plot
  • grouping (type=auto;pgarg;readonly): Defines the basic groups to investigate the metabolic activity.
    Defaults to ScrnaMetabolicLandscape.grouping
  • grouping_prefix (type=auto;pgarg;readonly): Default: "".
    Working as a prefix to group names.
    Defaults to ScrnaMetabolicLandscape.grouping_prefix
  • subsetting (type=auto;pgarg;readonly): How do we subset the data.
    Another column(s) in the metadata.
    Defaults to ScrnaMetabolicLandscape.subsetting
  • subsetting_prefix (type=auto;pgarg;readonly): Working as a prefix to subset names.
    Defaults to ScrnaMetabolicLandscape.subsetting_prefix