calour.export_html.export_html¶

calour.export_html.export_html(exp: calour.experiment.Experiment, sample_field=None, feature_field=None, title=None, xticklabel_len=50, cmap=None, clim=None, transform=<function log_n>, output_file='out', html_template=None, **kwargs)[source]¶

Export an interactive html heatmap for the experiment.

Creates a standalone html file with interactive d3.js heatmap of the experiment and interface to dbBact.

Note

This function is also available as a class method Experiment.export_html()

Parameters:

Parameters:	exp (Experiment) – Input experiment object. sample_field (str or None, optional) – The field to display on the x-axis (sample). None (default) to not show x labels. str to display field values for this field. feature_field (str or None, optional) – Name of the field to display on the y-axis (features) or None not to display names title (None or str (optional)) – None (default) to show experiment description field as title. str to set title to str. xticklabel_len (int, optional or None) – The maximal length for the x label strings (will be cut to this length if longer). Used to prevent long labels from taking too much space. None indicates no cutting cmap (None or str, optional) – None (default) to use mpl default color map. str to use colormap named str. clim (tuple of (float, float) or None, optional) – the min and max values for the heatmap or None to use all range. It uses the min and max values in the `data` array by default. transform (function, optional) – The transform function to apply to the data before plotting. default is log_n output_file (str, optional) – Name of the output html file (no .html ending - it will be appended). html_template (str or None, optional) – Name of the html template to use. None to use the default export_html_template.html template

exp (Experiment) – Input experiment object.
sample_field (str or None, optional) – The field to display on the x-axis (sample). None (default) to not show x labels. str to display field values for this field.
feature_field (str or None, optional) – Name of the field to display on the y-axis (features) or None not to display names
title (None or str (optional)) – None (default) to show experiment description field as title. str to set title to str.
xticklabel_len (int, optional or None) – The maximal length for the x label strings (will be cut to this length if longer). Used to prevent long labels from taking too much space. None indicates no cutting
cmap (None or str, optional) – None (default) to use mpl default color map. str to use colormap named str.
clim (tuple of (float, float) or None, optional) – the min and max values for the heatmap or None to use all range. It uses the min and max values in the data array by default.
transform (function, optional) – The transform function to apply to the data before plotting. default is log_n
output_file (str, optional) – Name of the output html file (no .html ending - it will be appended).
html_template (str or None, optional) – Name of the html template to use. None to use the default export_html_template.html template