Docstring:
Usage: qiime ps-plot zenrich [OPTIONS]
Creates a scatterplot of enriched peptides, points are colored according to
the z score thresholds provided. Scatterplot is layered over a heatmap
containing all of the data.
Inputs:
--i-data ARTIFACT FeatureTable[Normed]
FeatureTable containing normalized read counts of
samples and peptides. First column header must be
'Sequence Name' as produced by pepsirf. [required]
--i-zscores ARTIFACT FeatureTable[Zscore]
FeatureTable containing z scores of the normalized
read counts. Fist column header must be 'Sequence
Name' as produced by pepsirf. [required]
--i-highlight-probes ARTIFACT
InfoSNPN A InfoSNPN file that contains a list of probes/
peptides to highlight. [optional]
--i-negative-data ARTIFACT FeatureTable[Normed]
FeatureTable containing normalized read counts of
controls and peptides. First column header must be
'Sequence Name' as produced by pepsirf. [optional]
Parameters:
--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 Filename of file that contains peptide metadata
arguments will be related to data to be plotted. First column header
merged) must be id or one of the options found on:
https://docs.qiime2.org/2021.11/tutorials/metadata/?#i
dentifier-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-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-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 zenrich
Docstring:
Z Enrichment Variance Visualizer
Creates a scatterplot of enriched peptides, points are colored according to
the z score thresholds provided. Scatterplot is layered over a heatmap
containing all of the data.
Parameters
----------
data : FeatureTable[Normed]
FeatureTable containing normalized read counts of samples and peptides.
First column header must be 'Sequence Name' as produced by pepsirf.
zscores : FeatureTable[Zscore]
FeatureTable 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
highlight_probes : InfoSNPN, optional
A InfoSNPN file that contains a list of probes/ peptides to highlight.
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 : FeatureTable[Normed], optional
FeatureTable containing normalized read counts of controls and
peptides. First column header must be 'Sequence Name' as produced by
pepsirf.
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
-------
visualization : Visualization
