2.1. Usage (FastDTLgoea)

Install

FastDTLgoea is installed together with FastDTLmapper.

pip install fastdtlmapper

Additionally, FastDTLmapper requires GraphViz and InterProScan.

Install GraphViz

GraphViz is visualization library used in GOAtools.
In Ubuntu20.04, user can install GraphViz using apt command below.

sudo apt install graphviz

Install InterProScan

InterProScan is used as GOterms annoatation tool in FastDTLgoea.
Please refer to the following link to install latest InterProScan.
After installation, add PATH to InterProScan run script (interproscan.sh).

InterProScan - Installation requirements

Analysis Pipeline

This is brief description of analysis pipeline. See here for details.

1. Annotate GOterm to genomic protein CDS using InterProScan
2. Associate OG(Ortholog Group) & GOterm
3. Prepare each node gain/loss GOterm study-population data
4. Run each node gain/loss gene GOEA using GOAtools
5. Plot each node significant gain/loss GOterm using GOAtools()

Command Usage

Basic Command

FastDTLgoea inputs FastDTLmapper result directory.

FastDTLgoea -i [FastDTLmapper result directory]

Options

-h, --help          show this help message and exit
-i IN, --indir IN   FastDTLmapper result directory
--plot_pvalue_thr   Plot GOterm pvalue threshold (Default: 0.05)
--plot_max_num      Plot GOterm max number (Default: 10)
--plot_format       Plot file format [png|svg|jpg|pdf] (Default: 'png')
--plot_color        Plot specified hexcolor [e.g. '1affdb'] (Default: yellow to red gradient color)
--adjusted_pvalue   Use BH adjusted pvalue for plot threshold

Example Command

Run FastDTLmapper first. Then run FastDTLgoea with output directory of FastDTLmapper as input.

FastDTLmapper -i example/mycoplasma_dataset/fasta -t example/mycoplasma_dataset/species_tree.nwk -o mycoplasma_result
FastDTLgoea -i mycoplasma_result

Result of FastDTLgoea is newly output to 04_functional_analysis directory as shown below.
See here for 04_functional_analysis contents details.

.
├── 00_user_data/  
├── 01_orthofinder/ 
├── 02_dtl_reconciliation/  
├── 03_aggregate_map_result/  
├── 04_functional_analysis/  -- GOEA(GO Enrichment Analysis) result
│   ├── go_annotation/   -- InterProScan GOterm annotation result 
│   ├── go_enrichment/   -- Gain/Loss gene GOEA result
│   └── result_summary/  -- GOEA summary result
└── log/