Getting Started

Install From Source

The simplest installation path is:

git clone https://github.com/douymLab/INSIGHT.git
cd INSIGHT
pip install .

For local development:

pip install -e .

Runtime Dependencies

Python

In-Sight is packaged as a Python project and installs its Python dependencies from pyproject.toml.

R

Several plotting layouts depend on R packages. At minimum, make sure Rscript is available:

Rscript --version

The project currently expects packages such as:

• ggplot2
• aplot
• dplyr
• tidyr
• purrr
• readr
• gtable
• ragg
• ggfittext
• ggnewscale
• stringr
• scales

See README.md for the current installation suggestions.

First Command To Try

After installation:

plot2insights --help

Then list the built-in layouts:

plot2insights --list-layouts

If you want to see the bundled R script behind a layout:

plot2insights --layout base --show-r-script

Start From BAM Or Start From CSV

Use BAM mode if you are a normal user and your inputs are:

• BAM/CRAM
• reference FASTA
• one or more genomic regions

Use CSV mode only if you already have normalized plotting tables:

• base_df
• read_df
• reference_df

For most users, BAM mode is the primary interface.