Wiki Example Code Seems Outdated

[DarioS]

In Feature-level Analysis, I see generate_taxa_volcano_single example but function is not present in version 1.2 on CRAN.

> library(MicrobiomeStat)
> generate_taxa_volcano_single
Error: object 'generate_taxa_volcano_single' not found

Also, is there plan to add MA plot to package? It would be a nice addiiton.

[cafferychen777]

Dear Dario,

Thank you for reaching out regarding the generate_taxa_volcano_single function and the MA plot feature in the MicrobiomeStat package.

Please note that the MicrobiomeStat package is currently under active development, and many of the latest features have not yet been released to CRAN. To access the most up-to-date functionality, including the generate_taxa_volcano_single function, we recommend using the GitHub version of the package.

For detailed instructions on setting up the GitHub version of MicrobiomeStat, please refer to our installation guide: "https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/kick-start-your-journey-the-microbiomestat-installation-guide"

Regarding the MA plot, we appreciate your suggestion and will consider adding this feature in a future release of the package.

If you have any further questions or concerns, please don't hesitate to reach out.

Best regards,
Chen

[DarioS]

It is confusing because main branch is version 1.1.3. So, I thought CRAN is newer than GitHub because 1.2 is larger than 1.1.3.

[cafferychen777]

Hi Dario,

I apologize for the confusion caused by the inconsistent versioning between the CRAN and GitHub releases of MicrobiomeStat.

You're correct that the main branch on GitHub is labeled as version 1.1.3, while the CRAN version is 1.2. However, the GitHub version actually contains more recent features and updates than the CRAN release, despite having an older version number.

This discrepancy is an oversight on my part. I should have updated the version number on GitHub to reflect the latest changes. I will rectify this as soon as possible to ensure clarity and consistency across the different release channels.

To summarize:

• The GitHub version, although labeled 1.1.3, is the most up-to-date and includes features like generate_taxa_volcano_single that are not yet available in the CRAN release.
• I will update the GitHub version number to properly reflect its current state and avoid further confusion.

Thank you for bringing this issue to my attention. I appreciate your understanding and patience as I work to resolve the versioning inconsistency.

Best regards,
Caffery

[cafferychen777]

Dear Dario,

Great news! I'm pleased to inform you that we have just added the MA plot functionality to the MicrobiomeStat package, as you suggested. The new function generate_taxa_ma_plot_single has been implemented and is now available in the latest GitHub version of the package.

This function creates MA plots to visualize differential abundance analysis results, displaying the log2 fold change (M) against the average abundance (A) for each taxon. It's particularly useful for identifying taxa with significant abundance differences between groups while accounting for their baseline abundance levels.

Here's a simple example of how to use the new function:

# Load the package (GitHub version)
library(MicrobiomeStat)

# Run differential abundance analysis
test.list <- generate_taxa_test_single(
  data.obj = ecam.obj,
  group.var = "delivery",
  feature.level = c("Genus")
)

# Generate MA plot
plot.list <- generate_taxa_ma_plot_single(
  data.obj = ecam.obj,
  group.var = "delivery",
  test.list = test.list,
  feature.sig.level = 0.05,
  feature.mt.method = "fdr"
)

# View the plot
print(plot.list$Genus[[1]])

The function includes various customization options, such as adjusting significance levels, multiple testing correction methods, and color schemes.

Thank you for your valuable suggestion that helped improve the MicrobiomeStat package. We're committed to continuously enhancing the package based on user feedback and needs.

Best regards,
Chen