Docstring:
Usage: qiime ps-plot proteinHeatmap [OPTIONS]
Creates a heatmap based on the alignment of peptides in the enriched
peptides.
Inputs:
--i-enriched-dir ARTIFACT
PairwiseEnrichment A PairwiseEnrichment semantic type or .qza. This
file is the output of q2-pepsirf's enrich module
[required]
--i-protein-alignment ARTIFACT
ProteinAlignment A directory containing a tab delimited file
containing the protein and the filepath to the
associated alignment file. The file should start with
the header as 'ProtName' and be named 'manifest.tsv'.
And the files containing the protein alignment
information [required]
Parameters:
--p-enriched-suffix TEXT
The outfile suffix of the enriched peptide files.
[default: '_enriched.txt']
--p-align-header TEXT The name of the header to which identifies the
alignment positions separated by the align-delim
(Example column: '1~2~3~4'). [default: 'AlignPos']
--p-align-delim TEXT The deliminator that separates the alignment
positions. [default: '~']
--p-include-species / --p-no-include-species
Use if alignment file(s) include a 'Species' column.
[default: False]
--p-species-header TEXT
The name of the header to which identifies the
species column [default: 'Species']
--p-color-scheme TEXT String of the name of a color scheme for the
heatmap. Color schemes can be found here:
https://vega.github.io/vega/docs/schemes/
[default: 'viridis']
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 proteinHeatmap
Docstring:
Protein Alignment Heatmap
Creates a heatmap based on the alignment of peptides in the enriched
peptides.
Parameters
----------
enriched_dir : PairwiseEnrichment
A PairwiseEnrichment semantic type or .qza. This file is the output of
q2-pepsirf's enrich module
protein_alignment : ProteinAlignment
A directory containing a tab delimited file containing the protein and
the filepath to the associated alignment file. The file should start
with the header as 'ProtName' and be named 'manifest.tsv'. And the
files containing the protein alignment information
enriched_suffix : Str, optional
The outfile suffix of the enriched peptide files.
align_header : Str, optional
The name of the header to which identifies the alignment positions
separated by the align_delim (Example column: '1~2~3~4').
align_delim : Str, optional
The deliminator that separates the alignment positions.
include_species : Bool, optional
Use if alignment file(s) include a 'Species' column.
species_header : Str, optional
The name of the header to which identifies the species column
color_scheme : Str, optional
String of the name of a color scheme for the heatmap. Color schemes can
be found here: https://vega.github.io/vega/docs/schemes/
Returns
-------
visualization : Visualization
