An interactive vizualization to explore different parameters to PHATE
pip install -U git+https://github.com/FranckLejzerowicz/Xphate.git
- python >= 3.6
- PHATE (python implentation)
-i, --i-table TEXT Features table, input path.
-j, --i-res TEXT Table to make figure from.
-o, --o-html TEXT Visualization html, output path. [required]
-m, --m-metadata TEXT Sample metadata table.
-l, --p-labels TEXT Sample metadata column(s) to use for
labeling.
-c, --p-column TEXT Column from metadata `-m` to use for
filtering based on values of `-v`.
-v, --p-column-value TEXT Filtering value to select samples based on
column passed to `-c`.
-q, --p-column-quant INTEGER Filtering quantile / percentile for samples
based on column passed to `-c` (must be
between 0 and 100).
-fp, --p-filter-prevalence FLOAT
Filter features based on their minimum
sample prevalence (number >1 for sample
counts: <1 for samples fraction).
-fa, --p-filter-abundance FLOAT
Filter features based on their minimum
sample abundance (number >1 for abundance
counts: <1 for abundance fraction).
-f, --p-filter-order [meta-filter|filter-meta]
Order to apply the filters: 'filter-meta'
first the prevalence/abundance and then
based on variable; 'meta-filter' first based
on variable and then the
prevalence/abundance on the remaining.
[default: meta-filter]
-t, --p-ts INTEGER Min, Max and Step for the `t` parameter.
-d, --p-decays INTEGER Min, Max and Step for the `decay` parameter.
-k, --p-knns INTEGER Min, Max and Step for the `knns` parameter.
-n, --p-cpus INTEGER Number of jobs.
--verbose / --no-verbose
--version Show the version and exit.
--help Show this message and exit.
contact flejzerowicz@health.ucsd.edu