MetabolicPathwayActivity

This process calculates the pathway activities in different groups and subsets.

The cells are first grouped by subsets and then the metabolic activities are examined for each groups in different subsets.

For each subset, a heatmap and a violin plot will be generated.
The heatmap shows the pathway activities for each group and each metabolic pathway

MetabolicPathwayActivity_heatmap

The violin plot shows the distribution of the pathway activities for each group

MetabolicPathwayActivity_violin

Environment Variables

  • ntimes (type=int): Default: 5000.
    Number of times to do the permutation
  • ncores (type=int;pgarg): Default: 1.
    Number of cores to use for parallelization Defaults to ScrnaMetabolicLandscape.ncores
  • heatmap_devpars (ns): Device parameters for the heatmap
    • width (type=int): Width of the heatmap
    • height (type=int): Height of the heatmap
    • res (type=int): Resolution of the heatmap
  • violin_devpars (ns): Device parameters for the violin plot
    • width (type=int): Width of the violin plot
    • height (type=int): Height of the violin plot
    • res (type=int): Resolution of the violin plot
  • gmtfile (pgarg): The GMT file with the metabolic pathways.
    Defaults to ScrnaMetabolicLandscape.gmtfile
  • grouping (type=auto;pgarg;readonly): Defines the basic groups to investigate the metabolic activity, typically the clusters.
    Defaults to ScrnaMetabolicLandscape.grouping
  • grouping_prefix (type=auto;pgarg;readonly): Default: "".
    Working as a prefix to group names. For example, if we have grouping_prefix = "cluster" and we have 1 and 2 in the grouping column, the groups will be named as cluster_1 and cluster_2.
    Defaults to ScrnaMetabolicLandscape.grouping_prefix
  • subsetting (type=auto;pgarg;readonly): How do we subset the data. Other columns in the metadata to do comparisons. For example, "TimePoint" or ["TimePoint", "Response"].
    Defaults to ScrnaMetabolicLandscape.subsetting
  • subsetting_prefix (type=auto;pgarg;readonly): Working as a prefix to subset names.
    For example, if we have subsetting_prefix = "timepoint" and we have pre and post in the subsetting column, the subsets will be named as timepoint_pre and timepoint_post.
    If subsetting is a list, then this should also be a same-length list. If a single string is given, it will be repeated to a list with the same length as subsetting.
    Defaults to ScrnaMetabolicLandscape.subsetting_prefix