Docstring:
Usage: qiime ps-plot mutantScatters-tsv [OPTIONS]
Creates a scatterplot for mutant peptides with tsv filepaths 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. [required]
--m-metadata-file METADATA...
(multiple arguments The peptide metadata file that contains all of the
will be merged) positions, peptides, references, etc. [required]
--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. [required]
--p-reference-file-filepath TEXT
A file containing the reference peptide/ probe
along with the peptide/probe sequence. Must start
with 'CodeName'. [optional]
--p-peptide-header TEXT The name of the header of the pepides.
[default: 'FeatureID']
--p-reference-header TEXT
The name of the header of the references
[default: 'Reference']
--p-x-axis-header TEXT The name of the header of the x-axis positions to
be plotted [default: 'Position']
--p-category-header TEXT
The name of the header of the category to color the
points by [default: 'Category']
--p-label-header TEXT The name of the header that conatins the label for
the tooltip [default: 'Label']
--p-x-axis-label TEXT The name to title the x-axis [default: 'Position']
--p-y-axis-label TEXT The name to title the y-axis
[default: 'Mean Zscore']
--p-min-wobble NUMBER The minimum range of the wobble [default: -0.4]
--p-max-wobble NUMBER The maximum range of the wobble [default: 0]
--p-wobble / --p-no-wobble
Include this flag if you would like the points to
be on a wobble [default: False]
--p-scatter-only / --p-no-scatter-only
Include this flag if you only want to view the
scatterplot [default: True]
--p-scatter-boxplot / --p-no-scatter-boxplot
Include this flag if you want to view the
scatterplot and the corresponding boxplot.
[default: False]
--p-boxplot-only / --p-no-boxplot-only
Include this flag if you only want to view the
boxplot [default: False]
Outputs:
--o-mutant-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 mutantScatters_tsv
Docstring:
Mutant Scatters
Creates a scatterplot for mutant peptides with tsv filepaths instead of QZA
files
Parameters
----------
source : MetadataColumn[Categorical]
Metadata file containing all sample names and their source groups.
metadata : Metadata
The peptide metadata file that contains all of the positions, peptides,
references, etc.
zscore_filepath : Str
TSV file containing z scores of the normalized read counts. Fist column
header must be 'Sequence Name' as produced by pepsirf.
reference_file_filepath : Str, optional
A file containing the reference peptide/ probe along with the
peptide/probe sequence. Must start with 'CodeName'.
peptide_header : Str, optional
The name of the header of the pepides.
reference_header : Str, optional
The name of the header of the references
x_axis_header : Str, optional
The name of the header of the x-axis positions to be plotted
category_header : Str, optional
The name of the header of the category to color the points by
label_header : Str, optional
The name of the header that conatins the label for the tooltip
x_axis_label : Str, optional
The name to title the x-axis
y_axis_label : Str, optional
The name to title the y-axis
min_wobble : Float, optional
The minimum range of the wobble
max_wobble : Float, optional
The maximum range of the wobble
wobble : Bool, optional
Include this flag if you would like the points to be on a wobble
scatter_only : Bool, optional
Include this flag if you only want to view the scatterplot
scatter_boxplot : Bool, optional
Include this flag if you want to view the scatterplot and the
corresponding boxplot.
boxplot_only : Bool, optional
Include this flag if you only want to view the boxplot
Returns
-------
mutant_scatters_vis : Visualization
