HorGeneVis: Horizontal Gene Transfer Visualization

This R toolbox involves the analysis of horizontal gene transfer (HGT) between individual taxonomic categories using genomic data. The analysis is performed using R version 4.1.3.

Analysis Overview

The analysis involves several steps:

1. Initialization of Matrix: The initial matrix is created from a genome list file, with rows and columns corresponding to unique genome IDs.

2. Processing Phylogenetic Tree: The phylogenetic tree file is processed to extract new names, which are matched with the column names of the matrix.

3. Adding Entries to Matrix: Entries are added to the matrix based on the genome pairs obtained from the initial matrix.

4. Final Matrix Processing: The final matrix is processed based on a tree list file to match the column names and fill the matrix.

5. Heatmap Generation: Heatmaps are generated from the final matrix to visualize the results.

Installation

HorGeneVis can be installed from GitHub by running following command in R, but devtools is required.

# install.packages("devtools")
devtools::install_github("https://github.com/JanaSchwarzerova/HorGeneVis")

Functions

create_initial_matrix()

Function to create an initial matrix from a genome list file.

process_tree()

Function to process a phylogenetic tree file and extract new names.

add_entries_to_matrix()

Function to add entries to the matrix based on the genome pairs.

process_final_matrix()

Function to process the final matrix based on a tree list file.

generate_heatmap()

Function to generate a heatmap from a matrix.

Example Usage

HorGeneVis contains example data which were used to demonstrate its functionality. Use HorGeneVis_example_data() function to access them.

# Example data
cd_hit_file <- HorGeneVis_example_data("HGT_output_CD_hit.txt")
tree_file <- HorGeneVis_example_data("PhylogeneticTree_newick.txt")
tree_list_file <- HorGeneVis_example_data("Tree_list_Rectangular_output_IToL.txt")

Then continue with further analysis.

# Process the HGT genome list to create the initial matrix
initial_matrix <- create_initial_matrix(cd_hit_file)

# Call the function to process the tree file and extract new names
new_names <- process_tree(tree_file, initial_matrix)

# Add entries to the matrix based on the genome pairs
new_df <- add_entries_to_matrix(initial_matrix)

# Final processing of matrix as core for heat map visualization
final_mFin_ff_p <- process_final_matrix(tree_list_file, new_df)

# Example usage:
# Generate heatmap using the default "Blues" palette and 25 colors
generate_heatmap(final_mFin_ff_p)

# Generate heatmap using the "Greens" palette and 25 colors
generate_heatmap(final_mFin_ff_p, palette = "Greens")

# Generate heatmap using the "BrBG" palette and 25 colors
generate_heatmap(final_mFin_ff_p, palette = "BrBG")

# Generate heatmap using the "Accent" palette and 25 colors
generate_heatmap(final_mFin_ff_p, palette = "Accent")

# Generate chord diagram
create_chord_diagram(new_df[1:15, 16:20])

References

1. Schwarzerova, J., Rajasekaran, L., Jureckova, K., Nejezchlebova, J., Varga, M., Provaznik, V., et al. (2024). “Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria,” in Bioinformatics and Biomedical Engineering, 1–11. doi:10.1007/978-3-031-64636-2_20.
2. Schwarzerova, J., Zeman, M., Babak, V., Jureckova, K., Nykrynova, M., Varga, M., et al. (2024). Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Microbiol. Spectr. 12, e01964-23. doi:10.1128/spectrum.01964-23.