Docstring:
Usage: qiime ps-plot repScatters-tsv [OPTIONS]
Creates a scatterplot for reps of Col-sum data or reps of z score data wih
TSV files instead of QZA files
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-zscore-filepath TEXT
TSV file containing z scores of the normalized read
counts. Fist column header must be 'Sequence Name'
as produced by pepsirf. [optional]
--p-col-sum-filepath TEXT
TSV file containing normalized read counts of
samples and peptides. First column header must be
'Sequence Name' as produced by pepsirf. [optional]
--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-rep-scatters-vis 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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--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.pipelines import repScatters_tsv
Docstring:
Rep Scatter TSV
Creates a scatterplot for reps of Col-sum data or reps of z score data wih
TSV files instead of QZA files
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_filepath : Str, optional
TSV file containing z scores of the normalized read counts. Fist column
header must be 'Sequence Name' as produced by pepsirf.
col_sum_filepath : Str, optional
TSV file 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
-------
rep_scatters_vis : Visualization
