Docstring:
Usage: qiime ps-plot volcano [OPTIONS]
Generates a volcano plot given x and y values. Significant points will be
highlighted is identifiers are provided.
Parameters:
--p-x NUMBERS... Coordinates along the x-axis at which to plot
List[Float] points. [optional]
--p-y NUMBERS... Coordinates along the y-axis at which to plot
List[Float] points. [optional]
--p-taxa TEXT... List of identifiers, positionally associated with
List[Str] passed p-values and enrichment scores. These
identifiers will be displayed when the user mouses
over a point in the chart. [optional]
--p-xy-dir TEXT Directory containing tab delimited (TSV) files with
plotting data. Provide this as an alternative if
many plots are required. [optional]
--p-xy-access TEXT... List with column names in the tables collected in
List[Str] the 'xy-dir' which should be used to grab x and y
values, respectively. Refer to default as an
example. Only list length of 2 is supported.
[default: ['x', 'y']]
--p-taxa-access TEXT Column name in tables collected in the 'xy-dir'
which should be used to grab highlighting
information. [optional]
--p-x-threshold NUMBER Specifies the minimum ES a taxa can have in order
to be highlighted in the plot. If a taxa's ES is
less than the provided threshold, then the taxa is
not eligible to be highlighted. Please note the taxa
must also have a p-value less than the provided
p-value threshold to also be eligible for
highlighting. [default: 0.4]
--p-y-threshold NUMBER Specifies the maximum p-value a taxa can have in
order to be highlighted in the plot. If a taxa's
p-value is greater than the provided threshold, then
the taxa is not eligible to be highlighted. Please
note the taxa must also have an ES greater than the
provided ES threshold to also be eligible for
highlighting. [default: 0.05]
--p-log / --p-no-log Specifies whether to or not transform y values. If
True, the log (base 10) of the y values will be
plotted in ascending order; otherwise, the passed y
values will be plotted in descending order.
[default: True]
--p-xy-labels TEXT... Name of plot's x- and y-axis labels, respectively.
List[Str] [default: ['x', 'y']]
--p-titles TEXT... List of chart titles. These will be used to
List[Str] determine the names in the drop down which is used
to change chart views. [default: ['']]
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 volcano
Docstring:
Volcano Visualizer
Generates a volcano plot given x and y values. Significant points will be
highlighted is identifiers are provided.
Parameters
----------
x : List[Float], optional
Coordinates along the x-axis at which to plot points.
y : List[Float], optional
Coordinates along the y-axis at which to plot points.
taxa : List[Str], optional
List of identifiers, positionally associated with passed p-values and
enrichment scores. These identifiers will be displayed when the user
mouses over a point in the chart.
xy_dir : Str, optional
Directory containing tab delimited (TSV) files with plotting data.
Provide this as an alternative if many plots are required.
xy_access : List[Str], optional
List with column names in the tables collected in the 'xy_dir' which
should be used to grab x and y values, respectively. Refer to default
as an example. Only list length of 2 is supported.
taxa_access : Str, optional
Column name in tables collected in the 'xy_dir' which should be used to
grab highlighting information.
x_threshold : Float, optional
Specifies the minimum ES a taxa can have in order to be highlighted in
the plot. If a taxa's ES is less than the provided threshold, then the
taxa is not eligible to be highlighted. Please note the taxa must also
have a p-value less than the provided p-value threshold to also be
eligible for highlighting.
y_threshold : Float, optional
Specifies the maximum p-value a taxa can have in order to be
highlighted in the plot. If a taxa's p-value is greater than the
provided threshold, then the taxa is not eligible to be highlighted.
Please note the taxa must also have an ES greater than the provided ES
threshold to also be eligible for highlighting.
log : Bool, optional
Specifies whether to or not transform y values. If True, the log (base
10) of the y values will be plotted in ascending order; otherwise, the
passed y values will be plotted in descending order.
xy_labels : List[Str], optional
Name of plot's x- and y-axis labels, respectively.
titles : List[Str], optional
List of chart titles. These will be used to determine the names in the
drop down which is used to change chart views.
Returns
-------
visualization : Visualization
