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cafferychen777 committed Mar 21, 2024
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31 changes: 4 additions & 27 deletions README.Rmd
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Expand Up @@ -793,39 +793,16 @@ Remember, not finding significant results is also a result and can be informativ

With these strategies, you should be able to create a more readable and informative visualization, even when dealing with a large number of significant features.

### Issue 8: Error in pathway_daa with ALDEx2 method

When using the `pathway_daa` function with the ALDEx2 method, you may encounter the following error:

```
Error in Math.factor(c(3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 2L, 2L, 2L)) :
‘round’ not meaningful for factors
```

This issue may be related to recent updates in the ALDEx2 package that introduced compatibility issues with ggpicrust2. To resolve this issue, you can try installing ALDEx2 v.1.28 from the Bioconductor archive:

1. Remove the currently installed version of ALDEx2:
```r
remove.packages("ALDEx2")
```

2. Install ALDEx2 v.1.28:
```r
install.packages("https://mghp.osn.xsede.org/bir190004-bucket01/index.html#archive.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/ALDEx2/ALDEx2_1.28.0.tar.gz", repos = NULL, type = "source")
```

Alternatively, you can consider using another differential abundance analysis (daa) method, such as LinDA, until the compatibility issues are resolved.

## Author's Other Projects {#authors-other-projects}

1. [MicrobiomeGallery](https://cafferyyang.shinyapps.io/MicrobiomeGallery/): This is a web-based platform currently under development, which aims to provide a space for sharing microbiome data visualization code and datasets.
1. [MicrobiomeStat](https://www.microbiomestat.wiki/): The MicrobiomeStat package is a dedicated R tool for exploring longitudinal microbiome data. It also accommodates multi-omics data and cross-sectional studies, valuing the collective efforts within the community. This tool aims to support researchers through their extensive biological inquiries over time, with a spirit of gratitude towards the community’s existing resources and a collaborative ethos for furthering microbiome research.

![](https://raw.githubusercontent.com/cafferychen777/ggpicrust2_paper/main/paper_figure/MicrobiomeGallery_preview.jpg)
If you're interested in helping to test and develop MicrobiomeStat, please contact cafferychen7850@gmail.com.

2. [MicrobiomeStat](https://www.microbiomestat.wiki/): This is an R package that aims to provide new tools for microbiome analysis. The package is being developed with a particular focus on longitudinal studies, but it also includes tools for handling cross-sectional studies. While its primary purpose is to analyze microbiome data, it also has capabilities for handling multi-omics data. The goal is for MicrobiomeStat to become a widely-used tool for longitudinal analysis of multi-omics data. Please note that both the package and the accompanying wiki are still under development.
2. [MicrobiomeGallery](https://cafferyyang.shinyapps.io/MicrobiomeGallery/): This is a web-based platform currently under development, which aims to provide a space for sharing microbiome data visualization code and datasets.

If you're interested in helping to test and develop MicrobiomeStat, please contact cafferychen7850@gmail.com.
![](https://raw.githubusercontent.com/cafferychen777/ggpicrust2_paper/main/paper_figure/MicrobiomeGallery_preview.jpg)

We look forward to sharing more updates as these projects progress.
![](https://cdn.staticaly.com/gh/cafferychen777/ggpicrust2_paper/main/paper_figure/WeChatac562b362dadbf21a03414be3a5d06a5.png)
55 changes: 12 additions & 43 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -891,56 +891,25 @@ With these strategies, you should be able to create a more readable and
informative visualization, even when dealing with a large number of
significant features.

### Issue 8: Error in pathway_daa with ALDEx2 method

When using the `pathway_daa` function with the ALDEx2 method, you may
encounter the following error:

Error in Math.factor(c(3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 2L, 2L, 2L)) :
‘round’ not meaningful for factors

This issue may be related to recent updates in the ALDEx2 package that
introduced compatibility issues with ggpicrust2. To resolve this issue,
you can try installing ALDEx2 v.1.28 from the Bioconductor archive:

1. Remove the currently installed version of ALDEx2:

``` r
remove.packages("ALDEx2")
```

2. Install ALDEx2 v.1.28:

``` r
install.packages("https://mghp.osn.xsede.org/bir190004-bucket01/index.html#archive.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/ALDEx2/ALDEx2_1.28.0.tar.gz", repos = NULL, type = "source")
```
## Author’s Other Projects

Alternatively, you can consider using another differential abundance
analysis (daa) method, such as LinDA, until the compatibility issues are
resolved.
1. [MicrobiomeStat](https://www.microbiomestat.wiki/): The
MicrobiomeStat package is a dedicated R tool for exploring
longitudinal microbiome data. It also accommodates multi-omics data
and cross-sectional studies, valuing the collective efforts within
the community. This tool aims to support researchers through their
extensive biological inquiries over time, with a spirit of gratitude
towards the community’s existing resources and a collaborative ethos
for furthering microbiome research.

## Author’s Other Projects
If you’re interested in helping to test and develop MicrobiomeStat,
please contact <cafferychen7850@gmail.com>.

1. [MicrobiomeGallery](https://cafferyyang.shinyapps.io/MicrobiomeGallery/):
2. [MicrobiomeGallery](https://cafferyyang.shinyapps.io/MicrobiomeGallery/):
This is a web-based platform currently under development, which aims
to provide a space for sharing microbiome data visualization code
and datasets.

![](https://raw.githubusercontent.com/cafferychen777/ggpicrust2_paper/main/paper_figure/MicrobiomeGallery_preview.jpg)

2. [MicrobiomeStat](https://www.microbiomestat.wiki/): This is an R
package that aims to provide new tools for microbiome analysis. The
package is being developed with a particular focus on longitudinal
studies, but it also includes tools for handling cross-sectional
studies. While its primary purpose is to analyze microbiome data, it
also has capabilities for handling multi-omics data. The goal is for
MicrobiomeStat to become a widely-used tool for longitudinal
analysis of multi-omics data. Please note that both the package and
the accompanying wiki are still under development.

If you’re interested in helping to test and develop MicrobiomeStat,
please contact <cafferychen7850@gmail.com>.

We look forward to sharing more updates as these projects progress.

![](https://cdn.staticaly.com/gh/cafferychen777/ggpicrust2_paper/main/paper_figure/WeChatac562b362dadbf21a03414be3a5d06a5.png)

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