Docstring:
Usage: qiime ps-plot proteinHeatmap-dir [OPTIONS]
Creates a heatmap based on the alignment of peptides in the enriched
peptides with directory filepaths instead of QZA files.
Parameters:
--p-enriched-dir-filepath TEXT
Enriched directory filepath. This file is the
output of q2-pepsirf's enrich module. [required]
--p-protein-alignment-filepath TEXT
Filepath of the protein alignment manifest file.
The manifest file is tab delimited containing a
header with the column names 'ProtName' and
'AlignFile'. Each line specifies the protein and the
filepath to the associated alignment file.
[required]
--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-protein-heatmap-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 proteinHeatmap_dir
Docstring:
Protein Alignment Heatmap Dir
Creates a heatmap based on the alignment of peptides in the enriched
peptides with directory filepaths instead of QZA files.
Parameters
----------
enriched_dir_filepath : Str
Enriched directory filepath. This file is the output of q2-pepsirf's
enrich module.
protein_alignment_filepath : Str
Filepath of the protein alignment manifest file. The manifest file is
tab delimited containing a header with the column names 'ProtName' and
'AlignFile'. Each line specifies the protein and the filepath to the
associated alignment file.
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
-------
protein_heatmap_vis : Visualization
