gene-cluster-matrix 0.1.1

Visualization library for gene cluster & distance

Gene Cluster Matrix

Description

Gene cluter matrix is a command line tool to generate matrix that visualize distances between genes and gene clusters. The matrix is generated as interactive html file. This tool can also visualize phylogenetic tree and phylogenetically related & unrelated gene clusters.

Gene cluster matrix is developed by Python program and distributed under the MIT license.

Install

pip install --requirement https://raw.githubusercontent.com/slt666666/gene-cluster-matrix/main/requirements.txt ... install plotly pip install gene_cluster_matrix ... install other libraries

Dependencies

gene_cluster_matrix requires below libraries. (pip install automatically install dependencies)

• python (>= 3.6)
• numpy (>= 1.20.0)
• pandas (>= 1.2.0)
• plotly (>= 5.3.0)
• gffutils (>= 0.11.0)
• toytree (>= 2.0.1)
• Pillow (>= 9.2.0)

toyplot library is required to install independently.

• toyplot (>= 1.0.2.dev0)

ghostscript is required to generate phylogenetic tree image.

c.f.) Linux:sudo apt-get install ghostscript, Mac:brew install ghostscript

Usage examples

• simple distance matrix (the order is the given list order)

gene_cluster_matrix -g sample.gff3 -i id_list.txt -o output_name

• simple distance matrix by hand-made position data (the order is the given list order)

gene_cluster_matrix -p position.csv -i id_list.txt -o output_name

• distance matrix with phylogenetic tree & ids in tree are mRNA (the order is the given tree tips)

gene_cluster_matrix -g sample.gff3 -t sample.nwk -f mRNA -o output_name

• distance matrix with phylogenetic tree & clade information (the order is the given tree tips)

gene_cluster_matrix -g sample.gff3 -t sample.nwk -c clade.csv -o output_name

Input & Option

(required)
-g or -p … GFF3 fomrat file of reference genome (gff3 file) / position data file (csv file, format should be same as sample_data/position.csv)
-i or -t … Gene id list ordered by your preference (txt file) / phylogenetic tree file (newick format)
-o … Output file name (string)
(optional)
-d … Threshold distance to define gene cluster (int. default=50000)
-f … Specify gff feature type (gene or mRNA) of input ids (string. default=gene)
-c … Clade information for each gene/mRNA id. (csv file. format should be same as sample_data/clade.csv)

Output

XXX.html or XXX_with_tree.html … interactive html file that visualize gene cluster matrix
XXX_position.csv … position data for each id in input such as id_list or tree
XXX_tree.png … phylogenetic tree figure (if -t option is used)

Example

To view the examples, clone the gene_cluster_matrix repository and run by sample data:

$ git clone https://github.com/slt666666/gene_cluster_matrix.git
$ cd gene_cluster_matrix/sample_data
$ gene_cluster_matrix -g sample.gff3 -t sample.nwk -c clade.csv -f mRNA -o test

After running above commands, html file is generated in sample_data directory.

Licence

MIT

Author

Toshiyuki Sakai