Docstring:
Usage: qiime ps-plot repScatters [OPTIONS]
Creates a scatterplot for reps of Col-sum data or reps of z score data
Inputs:
--i-zscore ARTIFACT FeatureTable[Zscore]
FeatureTable containing z scores of the normalized
read counts. Fist column header must be 'Sequence
Name' as produced by pepsirf. [optional]
--i-col-sum ARTIFACT FeatureTable[Normed]
FeatureTable containing normalized read counts of
samples and peptides. First column header must be
'Sequence Name' as produced by pepsirf. [optional]
Parameters:
--m-source-file METADATA
--m-source-column COLUMN MetadataColumn[Categorical]
Metadata file containing all sample names and their
source groups. Used to create pairs tsv to run pepsirf
enrich module. [optional]
--p-user-spec-pairs TEXT...
List[Str] !!!Write a description!!! [optional]
--p-pn-filepath TEXT Filepath of .tsv pairs file generated by standalone
autopepsirf python script, containing all sample
pairings, typically ending in '_PN.tsv'. (Depricated)
[optional]
--p-plot-log / --p-no-plot-log
Use if you want axes to be shown on a log-scale.
[default: False]
--p-facet-charts / --p-no-facet-charts
Allows for view of all tables on one page instead of
the available dropdown menu. [default: False]
--p-xy-threshold INTEGER
Highlight the outliers of the plot and add a
hoverable tooltip to view what they are. [optional]
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 repScatters
Docstring:
Rep Scatter
Creates a scatterplot for reps of Col-sum data or reps of z score data
Parameters
----------
source : MetadataColumn[Categorical], optional
Metadata file containing all sample names and their source groups. Used
to create pairs tsv to run pepsirf enrich module.
user_spec_pairs : List[Str], optional
!!!Write a description!!!
pn_filepath : Str, optional
Filepath of .tsv pairs file generated by standalone autopepsirf python
script, containing all sample pairings, typically ending in '_PN.tsv'.
(Depricated)
plot_log : Bool, optional
Use if you want axes to be shown on a log-scale.
zscore : FeatureTable[Zscore], optional
FeatureTable containing z scores of the normalized read counts. Fist
column header must be 'Sequence Name' as produced by pepsirf.
col_sum : FeatureTable[Normed], optional
FeatureTable containing normalized read counts of samples and peptides.
First column header must be 'Sequence Name' as produced by pepsirf.
facet_charts : Bool, optional
Allows for view of all tables on one page instead of the available
dropdown menu.
xy_threshold : Int, optional
Highlight the outliers of the plot and add a hoverable tooltip to view
what they are.
Returns
-------
visualization : Visualization
