What it does

This module plots the raw data of the features detected by LEfSe as biomarkers as abundance histograms with class and subclass information. The features are exported as images and the user can download all the images in a .zip archive. It is also possible to export all the features (instead of the biomarkers only). For exporting or analyzing few features only the "Plot One Feature" module is recommended.

Input format

The module accepts two datasets: the data formatted with the "Format Input for LEfSe" module and the output of the LEfSe analysis. Both datasets are necessary to run the module.

Output format

The module generates zip archives containing images in png, svg or pdf format.

Advanced parameter settings

Graphical options

• Set the maximum y value: -1 means automatic parameter setting that is computed as the minimum between the highest abundance value and three times the highest subclass median.
• Set the minimum y value: -1 means automatic parameter setting that is computed as the maximum between 0 and the 90% of the smallest abundance value.
• Title font size: set the font size of the title only.
• Class font size: set the font of the legend for the class names and colors.
• Size of subclasses names and y values: set the font size for the axis labels.
• Width of the plot: horizontal size (in inches) of the plot.
• Height of the plot: vertical size (in inches) of the plot.
• Background color: whether to generate plots with black or white backgrounds, adjusting properly the other colors.
• Class label position: whether to place the class labels on the top or on the bottom of the plot.
• Plot subclass means (straight line): whether to plot the subclass means with straight horizontal lines.
• Plot subclass medians (dotted line): whether to plot the subclass medians with dotted horizontal lines.

Examples

Please see the examples reported for the "Plot One Feature" module (E). This module just produces multiple plots in the same way and compresses them into a .zip archive.