Chapter 2 Alpha diversity mapping description
2.1 Upload sample data
You need to upload two data files including alpha diversity result file and metadata file.
Such as
| Sample | berger_parker | buzas_gibson | chao1 | dominance | equitability | jost | jost1 | reads | richness | robbins | simpson | shannon_e | shannon_2 | shannon_10 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HSL001 | 0.059 | 0.0636 | 637.5 | 0.986 | 0.814 | 105.8 | 190.7 | 3000 | 631 | 0.541 | 0.014 | 5.25 | 7.58 | 2.28 |
| HSL003 | 0.0483 | 0.144 | 965.7 | 0.993 | 0.883 | 246.3 | 430.7 | 3000 | 961 | 0.554 | 0.00679 | 6.07 | 8.75 | 2.63 |
| HSL004 | 0.041 | 0.122 | 929.5 | 0.992 | 0.865 | 205.2 | 367.3 | 3000 | 922 | 0.587 | 0.00775 | 5.91 | 8.52 | 2.57 |
| HSL006 | 0.0613 | 0.055 | 545.5 | 0.985 | 0.813 | 96.4 | 165.1 | 3000 | 536 | 0.551 | 0.0153 | 5.11 | 7.37 | 2.22 |
| HSL010 | 0.185 | 0.0443 | 593.8 | 0.959 | 0.767 | 49.7 | 132.8 | 3000 | 587 | 0.56 | 0.041 | 4.89 | 7.05 | 2.12 |
| HSL013 | 0.104 | 0.0928 | 883.9 | 0.982 | 0.831 | 115.7 | 278.3 | 3000 | 876 | 0.597 | 0.0175 | 5.63 | 8.12 | 2.44 |
The first column is the sample id,the other column is the different alpha index values.
| SampleID | Group |
|---|---|
| HSL001 | HSL |
| HSL002 | HSL |
| HSL003 | HSL |
| HSL004 | HSL |
| HSL005 | HSL |
| HSL006 | HSL |
| HSL007 | HSL |
| HSL008 | HSL |
| HSL009 | HSL |
| HSL010 | HSL |
| HSL011 | HSL |
| HSL012 | HSL |
| HSL013 | HSL |
The first column is the sample id,the second column is the grouping of samples.
Paying attention, please ,you need to upload the file in the format of the sample data
2.2 Different alpha index values ,and statistical methods
After uploading your datas,you need to select which column in the first file you need to use for drawing,and the statistical methods you need to use.
Two methods based on t test and kruskal wallis test are performed on input data
2.3 Different drawing tools
2.3.1 box-plot
2.3.2 pirates
- The color palette of the plot. the name of a palette in the piratepal() function (e.g.; “basel,” “google,” “southpark”).
- Choose a different theme
2.3.3 cloudyrain
- This button allows you to choose whether to transpose the graphics.
The box diagram can be regarded as a cloud diagram, a box diagram, and raindrops composed of three parts; the positional relationship of the three components can be adjusted through the following parameters
With this parameter, you can adjust the raindrops to be above or below the axis of the cloud graph. The top is + and the bottom is -.
With this parameter you can adjust the width of the box chart.
With this parameter, you can adjust the box shape above or below the axis of the cloud graph. The top is + and the bottom is -.
With this parameter, you can adjust the distribution spacing on the horizontal axis of the raindrop graph.
With this parameter you can adjust the size of the raindrops.
2.3.4 violin
