Docstring:
Usage: qiime ps-plot zscatter [OPTIONS]
Creates a scatter plot using Z scores from two samples. A spline line can
also be added. Significant points can also be highlighted by passing
metadata, as well.
Inputs:
--i-zscores ARTIFACT FeatureTable[Zscore]
Matrix of Z scores. [required]
Parameters:
--p-pairs-file TEXT Tab delimited (TSV) file with a pair of sample
replicates on each line. [required]
--p-p-val-access TEXT Column name with data to compare to
'highlight-threshold' which will be considered for
highlighting. [optional]
--p-le-peps-access TEXT
Column name with data to use in tooltip. [optional]
--p-taxa-access TEXT Column name with taxa names to use when
highlighting. [optional]
--p-spline-file TEXT Tab delimited (TSV) file with spline results. The
first timepoint provides the x coordinates, and the
second provides the y coordinates. [optional]
--p-highlight-data TEXT
Path to a file or a directory with multiple files
which contain information needed to highlight
significant taxa. The file(s) should be tab delimited
(TSV format). [optional]
--p-highlight-threshold NUMBER
Maximum p-value a taxa can have to be highlighted.
Anything above this threshold will not be considered
'significant'. [default: 0.05]
Outputs:
--o-visualization VISUALIZATION
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.ps_plot.visualizers import zscatter
Docstring:
Z Score Scatter Visualization
Creates a scatter plot using Z scores from two samples. A spline line can
also be added. Significant points can also be highlighted by passing
metadata, as well.
Parameters
----------
zscores : FeatureTable[Zscore]
Matrix of Z scores.
pairs_file : Str
Tab delimited (TSV) file with a pair of sample replicates on each line.
p_val_access : Str, optional
Column name with data to compare to 'highlight_threshold' which will be
considered for highlighting.
le_peps_access : Str, optional
Column name with data to use in tooltip.
taxa_access : Str, optional
Column name with taxa names to use when highlighting.
spline_file : Str, optional
Tab delimited (TSV) file with spline results. The first timepoint
provides the x coordinates, and the second provides the y coordinates.
highlight_data : Str, optional
Path to a file or a directory with multiple files which contain
information needed to highlight significant taxa. The file(s) should be
tab delimited (TSV format).
highlight_threshold : Float, optional
Maximum p-value a taxa can have to be highlighted. Anything above this
threshold will not be considered 'significant'.
Returns
-------
visualization : Visualization
