[](https://anaconda.org/bioconda/methplotlib)
[](https://anaconda.org/bioconda/methplotlib)
# METHPLOTLIB
This script generates a browser view on a window using data from
i) [nanopolish](https://github.com/jts/nanopolish), either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.and scripts/split_calls_by_phase.py
ii) [nanocompore](https://github.com/tleonardi/nanocompore)
iii) in ont-cram format with MM/ML tags according to the SAM specifications
iv) in bedgraph format
## INSTALLATION
Creating a new conda environment:
`conda create -n methplotlib methplotlib`
Or using pip:
`pip install methplotlib`
## USAGE
```
methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
[NAMES ...] -w WINDOW [-g GTF] [-b BED] [-f FASTA]
[--simplify] [--split] [--static STATIC] [--smooth SMOOTH]
[--dotsize DOTSIZE] [--example] [-o OUTFILE] [-q QCFILE]
plotting nanopolish methylation calls or frequency
optional arguments:
-h, --help show this help message and exit
-v, --version Print version and exit.
-m, --methylation METHYLATION [METHYLATION ...]
data in nanopolish, nanocompore, ont-cram or bedgraph
format
-n, --names NAMES [NAMES ...]
names of datasets in --methylation
-w, --window WINDOW window (region) to which the visualisation has to be restricted
-g, --gtf GTF add annotation based on a gtf file
-b, --bed BED add annotation based on a bed file
-f, --fasta FASTA required when --window is an entire chromosome, contig or transcript
--simplify simplify annotation track to show genes rather than transcripts
--split split, rather than overlay the methylation tracks
--static Make a static image of the browser window (filename)
--binary Make the nanopolish plot ignorning log likelihood nuances
--smooth Rolling window size for averaging frequency values (int)
--dotsize Control the size of dots in the per read plots (int)
--example Show example command and exit.
-o, --outfile OUTFILE File to write results to. Default:
methylation_browser_{chr}_{start}_{end}.html. Use
{region} as a shorthand for {chr}_{start}_{end} in the
filename. Missing paths will be created.
-q, --qcfile QCFILE File to write the qc report to. Default: The path in
outfile prefixed with qc_, default is qc_report_methyl
ation_browser_{chr}_{start}_{end}.html. Use {region}
as a shorthand for {chr}_{start}_{end} in the
filename. Missing paths will be created.
```
## Snakemake workflow
For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.
## Example data
The `examples` folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.
## Companion scripts
The `scripts` folder contains scripts for phasing modification calls in haplotypes based on [WhatsHap](https://whatshap.readthedocs.io/en/latest/) phasing, allele specific modification testing for phased data and differential modification testing across subjects.
## TO DO - CONTRIBUTIONS WELCOME
- Outlier detection (in windows) across samples
Raw data
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