Introduction

This vignette demonstrates how to use the ggtaxplot package to process and visualize taxonomic data.

Installation

You can install the package from GitLab using the following command:

devtools::install_git("https://gitlab.com/ccoclet/ggtaxplot.git")

## Downloading git repo https://gitlab.com/ccoclet/ggtaxplot.git

## '/usr/bin/git' clone --depth 1 --no-hardlinks https://gitlab.com/ccoclet/ggtaxplot.git /var/folders/z2/0xq80m5x1cj8_wr_40gg7g2c0000gp/T//RtmpDjTT99/file11c3c496cde35

## 
## ── R CMD build ─────────────────────────────────────────────────────────────────
## * checking for file ‘/private/var/folders/z2/0xq80m5x1cj8_wr_40gg7g2c0000gp/T/RtmpDjTT99/file11c3c496cde35/DESCRIPTION’ ... OK
## * preparing ‘ggtaxplot’:
## * checking DESCRIPTION meta-information ... OK
## * checking for LF line-endings in source and make files and shell scripts
## * checking for empty or unneeded directories
## * building ‘ggtaxplot_0.0.1.tar.gz’

## Installing package into '/private/var/folders/z2/0xq80m5x1cj8_wr_40gg7g2c0000gp/T/Rtmpb88kQL/Rinst11c1238f1a29f'
## (as 'lib' is unspecified)

Example Usage

Load the Package

library(ggtaxplot)

Example Data

Here is an example dataset:

data <- data.frame(
    ID = c("ID1", "ID2", "ID3"),
    Taxonomy = c("d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia",
                 "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus",
                 "d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium")
)

Generate the Plot

plot <- ggtaxplot(data)

## Warning: Use of `filtered_vOTUs_vBins_Host_Prediction_t_color_df[[1]]` is discouraged.
## ℹ Use `.data[[1]]` instead.
## Use of `filtered_vOTUs_vBins_Host_Prediction_t_color_df[[1]]` is discouraged.
## ℹ Use `.data[[1]]` instead.

print(plot)

## Warning: Use of `filtered_vOTUs_vBins_Host_Prediction_t_color_df[[1]]` is discouraged.
## ℹ Use `.data[[1]]` instead.
## Use of `filtered_vOTUs_vBins_Host_Prediction_t_color_df[[1]]` is discouraged.
## ℹ Use `.data[[1]]` instead.

Conclusion

This vignette provided an overview of how to use the ggtaxplot package. For more details, refer to the package documentation.

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