Introduction

The Alpha diversity visualization is commonly used to view community diversity differences between groups, based on a box plot. The online Alpha diversity allows users to change to different taxonomy levels, add p-value, show scatter points or not, use violin plot or not.

If you have the raw profiling table of samples without differential testing analysis, you can use Alpha diversity module.

If you want to visualize your processed results, you can upload the following inputs to visualize online interactively:

Input Files

Click on the Download Data button to check the demo input files.

1. Diversity table (TSV file)

• header
  samples ID
• row names
  For each sample, the table would contain its alpha diversity of different taxonomy levels, from kingdom to strain.

2. Group information (TSV file)

• header
  

• rows
  sample ID and the group information for the corresponding sample.

3. P-value result (TSV file) (Optional)

• example
  A table of testing p-value at all taxonomy levels.

Display Interactions

• Drag P
  Drag the p notes to adjust its position.
• Tooltips
  Hover on the box and a info tooltip will show.
• Drag x axis labels
  When rotated x axis label is true, you can drag a label to adjust the rotation angle. The rotation rangle is from 0 to 90 degree with label anchored on right middle.
• Download
  One SVG file will be generated when the Download Chart button is clicked.

Editor Functions

• Files

  • Manage Files: checklist of files uploaded previously, delete or download files.
  • Upload: upload files. Note that the duplicated file name will be alerted and given a random postfix.
  • Choose: choose files uploaded previously.

• Data

  • Taxonomic Rank: select the rank of the data to display.
  • Range lower bound: edit the mininum of the value range.
  • Range upper bound: edit the maximum of the value range.

• Plot Settings

  • Plot Width: input a value to adjust the width of the plot.
  • Plot Height: input a value to adjust the height of the plot.
  • Label Font Size: input an integer to adjust the size of the x/y label.
  • Tick Font Size: input an integer to adjust the size of the axises ticks.
  • Rotate X Axis Labels: check the check box to rotate the x-axis labels.

• Box Settings

  • Customize Colors: adjust colors for the boxes, scatters, and violins.
  • Hollow box: check it to hollow boxes.
  • Outlier: check it to draw outliers.
  • P-value: check it to display the p notes.
  • Sample Scatters: check it to draw sample scatters over the boxes.
  • Draw Violin: check it to draw violins instead of boxes.

Manual version=1.0, written by Dr. JIANG Yiqi and Ms. WANG Yanfei on 2022-02-01.

Manual version=1.1, updated by Dr. JIANG Yiqi on 2022-04-19.