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ggtaxplot

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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