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YilingWang1997 / Global-Soil-Virome

Supporting code for manuscript: "Ecological/environmental drivers of global soil virome diversity"
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question about shannon #2

Open dsfchina opened 4 days ago

dsfchina commented 4 days ago

There are a few questions that have bothered me for a long time, although these questions seem to be not very professional, I hope to get your answers. 1: How do you calculate abundances at the family, genus, and species levels to calculate the shannon index. 2: Why is the range of the values of the Pearson correlation coefficient of Figure 4CD not between -1 and 1. Thanks!

YilingWang1997 commented 4 days ago

Thank you for your questions. Here's how we approach these aspects:

  1. Shannon Index Calculation: We calculate the Shannon index at the genus level by aggregating the abundances of species within the same genus, then computing the relative abundance at the genus level before applying the Shannon formula. Since the Shannon index incorporates abundance, the total number of individuals within a category may influence the result, leading to some inherent biases. While this method is not perfect and can introduce some limitations, it is provided here for your reference.

  2. Regarding the Slope Coefficient in Figure 4CD: We realized that there was an issue with the x-axis labeling in Figure 4CD, which should reflect the slope coefficient. The values were calculated using the lm function in R, and we apologize for any confusion caused by this error.