# NanoMethViz
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NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing.
## Installation
You can install NanoMethViz from Bioconductor with:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NanoMethViz")
```
To install the latest developmental version, use:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("NanoMethViz")
```
## Usage
This package currently works with data from megalodon, nanopolish and f5c, to import your data please see the following vignette
``` r
vignette("ImportingData", package = "NanoMethViz")
```
An introductory example for plotting can be found in the package vignette:
``` r
vignette("Introduction", package = "NanoMethViz")
```
Other vignettes are provided for various features:
``` r
# how to use dimensionality reduction plots
vignette("DimensionalityReduction", package = "NanoMethViz")
# how to import external annotations
vignette("ExonAnnotations", package = "NanoMethViz")
```
## Examples
### MDS Plot
The MDS plot is used to visualise differences in the methylation profiles of
multiple samples.
### Feature Aggregation
The feature aggregation plot can average the methylation profiles across a set
of features.
### Spaghetti plot
The spaghetti plot shows the smoothed methylation probabilities over a specific
region, along with the methylation probabilities along individual long reads.
### Heatmap
The heatmap shows methylation probabilities on individual sites along stacked
reads.
## License
This project is licensed under Apache License, Version 2.0.
