Docstring:
Usage: qiime ps-plot zenrich-tsv [OPTIONS]
Pipeline that converts .tsv files to .qza files and then runs zenrich.
Parameters:
--p-data-filepath TEXT Filepath of .tsv file containing normalized read
counts of samples and peptides. First column header
must be 'Sequence Name' as produced by pepsirf.
[required]
--p-zscores-filepath TEXT
Filepath of .tsv file containing z scores of the
normalized read counts. Fist column header must be
'Sequence Name' as produced by pepsirf. [required]
--p-flex-reps / --p-no-flex-reps
[default: False]
--p-negative-controls TEXT...
List[Str] Sample names of the negative controls to be used
(Example argument: --p-negative-controls sample1
sample2 sample3). [optional]
--p-negative-id TEXT [optional]
--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-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]
--m-peptide-metadata-file METADATA...
(multiple arguments Filename of file that contains peptide metadata
will be merged) related to data to be plotted. First column header
must be id or one of the options found on:
https://docs.qiime2.org/2021.11/tutorials/metadata/?
#identifier-column [optional]
--p-tooltip TEXT... List of title names found in the peptide metadata
List[Str] file to be added to the hover tooltip (Parameter is
case sensitive. Example argument: --p-tooltip
Species SpeciesID). 'Peptide' and 'Zscores' will
always be added to the list of titles, if peptide
metadata is not provided just 'Peptide' and
'Zscores' will be shown.
[default: ['Species', 'SpeciesID']]
--p-color-by TEXT A column within the metadata file to base the
coloring of the enriched peptide points. This
parameter is case sensitive and the default is the
different zscore thresholds.
[default: 'z_score_threshold']
--p-negative-data-filepath TEXT
Filepath of .tsv file containing normalized read
counts of controls and peptides. First column header
must be 'Sequence Name' as produced by pepsirf.
[optional]
--p-highlighted-probes-filepath TEXT
A InfoSNPN file that contains a list of
probes/peptides to highlight. [optional]
--p-step-z-thresh INTEGER
Range(1, None) Integar to increment z-score thresholds.
[default: 5]
--p-upper-z-thresh INTEGER
Range(2, None) Upper limit of z-score thresholds (non-inclusive).
[default: 30]
--p-lower-z-thresh INTEGER
Range(1, None) Lower limit of z-score thresholds (inclusive).
[default: 5]
--p-exact-z-thresh TEXT...
List[Str] List of exact z score thresholds either individual
or combined. List MUST BE in descending order.
(Example argument: '--p-exact-z-thresh 25 10 3' or
'--p-exact-z-thresh 6,25 4,10 1,3') [optional]
--p-exact-cs-thresh TEXT
A single col-sum threshold. Default 20.
[default: '20']
--p-pepsirf-binary TEXT The binary to call pepsirf on your system. Used to
call pepsirf enrich module. [default: 'pepsirf']
Outputs:
--o-zenrich-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 zenrich_tsv
Docstring:
zenrich TSV Pipeline
Pipeline that converts .tsv files to .qza files and then runs zenrich.
Parameters
----------
data_filepath : Str
Filepath of .tsv file containing normalized read counts of samples and
peptides. First column header must be 'Sequence Name' as produced by
pepsirf.
zscores_filepath : Str
Filepath of .tsv file containing z scores of the normalized read
counts. Fist column header must be 'Sequence Name' as produced by
pepsirf.
flex_reps : Bool, optional
negative_controls : List[Str], optional
Sample names of the negative controls to be used (Example argument:
--p-negative-controls sample1 sample2 sample3).
negative_id : Str, optional
source : MetadataColumn[Categorical], optional
Metadata file containing all sample names and their source groups. Used
to create pairs tsv to run pepsirf enrich module.
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)
peptide_metadata : Metadata, optional
Filename of file that contains peptide metadata related to data to be
plotted. First column header must be id or one of the options found on:
https://docs.qiime2.org/2021.11/tutorials/metadata/?#identifier-column
tooltip : List[Str], optional
List of title names found in the peptide metadata file to be added to
the hover tooltip (Parameter is case sensitive. Example argument:
--p-tooltip Species SpeciesID). 'Peptide' and 'Zscores' will always be
added to the list of titles, if peptide metadata is not provided just
'Peptide' and 'Zscores' will be shown.
color_by : Str, optional
A column within the metadata file to base the coloring of the enriched
peptide points. This parameter is case sensitive and the default is the
different zscore thresholds.
negative_data_filepath : Str, optional
Filepath of .tsv file containing normalized read counts of controls and
peptides. First column header must be 'Sequence Name' as produced by
pepsirf.
highlighted_probes_filepath : Str, optional
A InfoSNPN file that contains a list of probes/peptides to highlight.
step_z_thresh : Int % Range(1, None), optional
Integar to increment z-score thresholds.
upper_z_thresh : Int % Range(2, None), optional
Upper limit of z-score thresholds (non-inclusive).
lower_z_thresh : Int % Range(1, None), optional
Lower limit of z-score thresholds (inclusive).
exact_z_thresh : List[Str], optional
List of exact z score thresholds either individual or combined. List
MUST BE in descending order. (Example argument: '--p-exact-z-thresh 25
10 3' or '--p-exact-z-thresh 6,25 4,10 1,3')
exact_cs_thresh : Str, optional
A single col-sum threshold. Default 20.
pepsirf_binary : Str, optional
The binary to call pepsirf on your system. Used to call pepsirf enrich
module.
Returns
-------
zenrich_vis : Visualization
