Paired pairwise distance testing and boxplots
Performs pairwise distance testing between sample pairs from each subject.
Sample pairs may represent a typical intervention study, e.g., samples
collected pre- and post-treatment; paired samples from two different
timepoints (e.g., in a longitudinal study design), or identical samples
receiving different two different treatments. This action tests whether the
pairwise distance between each subject pair differs between groups (e.g.,
groups of subjects receiving different treatments) and produces boxplots of
paired distance distributions for each group.
Parameters
- distance_matrix : DistanceMatrix
- Matrix of distances between pairs of samples.
- metadata : Metadata
- Sample metadata file containing individual_id_column.
- group_column : Str
- Metadata column on which to separate groups for comparison
- state_column : Str
- Metadata column containing state (e.g., Time) across which samples are
paired.
- state_1 : Str
- Baseline state column value.
- state_2 : Str
- State column value to pair with baseline.
- individual_id_column : Str
- Metadata column containing subject IDs to use for pairing samples.
WARNING: if replicates exist for an individual ID at either state_1 or
state_2, that subject will be dropped and reported in standard output
by default. Set replicate_handling="random" to instead randomly select
one member.
- parametric : Bool, optional
- Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
- palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
- Color palette to use for generating boxplots.
- replicate_handling : Str % Choices('error', 'random', 'drop'), optional
- Choose how replicate samples are handled. If replicates are detected,
"error" causes method to fail; "drop" will discard all replicated
samples; "random" chooses one representative at random from among
replicates.
Returns
visualization : Visualization