Paired difference testing and boxplots
Performs paired difference testing between samples 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
change in a numeric metadata value "metric" differs from zero and differs
between groups (e.g., groups of subjects receiving different treatments),
and produces boxplots of paired difference distributions for each group. A
feature table artifact is required input, though whether "metric" is
derived from the feature table or metadata is optional.
Parameters
- metadata : Metadata
- Sample metadata file containing individual_id_column.
- metric : Str
- Numerical metadata or artifact column to test.
- 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.
- group_column : Str, optional
- Metadata column on which to separate groups for comparison
- 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.
- table : FeatureTable[RelativeFrequency], optional
- Feature table to optionally use for paired comparisons.
Returns
visualization : Visualization