pairwiseANIviz

Pairwise ANI (Average Nucleotide Identity) visulization tool. This tool is designed to help visualize the results of pairwise comparisons among multiple genomes.

First, Scipy is used to perform hierarchical/agglomerative clustering, followed by generating a clustermap using Seaborn that supports various Matplotlib colormaps.

Main features

• Support various matplotlib colormaps
• Taxonomic classification result can be included to illustrate different taxa
• Specific outrange ANI values can be set (eg. 95% ANI values)
• Multi-format outputs (JPG, PNG, TIFF, SVG, PDF, EPS)

Example

1. Using different matplotlib colormaps

2. With taxonomy indicated by different palettes

3. With ANI values illustrated

4. With outrange ANI values (95%) colored red

Installation

```shell

Dependencies: Matplotlib, Seaborn, Scipy, Pandas

Install pairwiseANIviz using pip

pip install pairwiseANIviz==1.3 ```

Usage

Options

```bash usage: pairwiseANIviz [options] anifile

positional arguments: anifile File containing pairwise ANI analysis result.

options: -h, --help show this help message and exit -v, --version Show pairwiseANIviz version number and exit. -o OUTDIR, --outdir OUTDIR Directory to save the output figures (default 'pairwiseANIviz'). --method {single,complete,average,weighted,centroid,median,ward} Linkage method to use for calculating clusters (default 'average'). See https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage --metric {braycurtis,canberra,chebyshev,cityblock,correlation,cosine,dice,euclidean,hamming,jaccard,jensenshannon,kulczynski1,mahalanobis,matching,minkowski,rogerstanimoto,russellrao,seuclidean,sokalmichener,sokalsneath,sqeuclidean,yule} The distance metric to use (default 'euclidean'). See https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist -cmap COLORMAP, --colormap COLORMAP Matplotlib colormap used when drawing the heatmap of ANI values (default 'Blues'). See https://matplotlib.org/stable/users/explain/colors/colormaps.html --figWidth FIGWIDTH Figure width (default '15'). --figHeight FIGHEIGHT Figure height (default '15'). --linewidth LINEWIDTH Line width of the main heatmap (default 0.5) --linecolor LINECOLOR Line color of the main heatmap (default 'grey'). --rowCluster Draw the row cluster. --colCluster Draw the column cluster. --annotation Show ANI values on the plot. --outrangeValue OUTRANGEVALUE Cells have ANI values over specific threshold set to red (eg. cells have ANI value >=0.95 set to red) (default 100). -c CLASSIFICATIONFILE, --classificationFile CLASSIFICATIONFILE File containing classification result generated by GTDBTk(https://github.com/Ecogenomics/GTDBTk). -t {domain,phylum,class,order,family,genus,species}, --taxaLevel {domain,phylum,class,order,family,genus,species} Taxa level illustrated on the plot. Choose from "domain, phylum, class, order, family, genus, species". Note that this parameter only works if classification result was input. --colorPalette COLORPALETTE Color palette used to return a specified number of evenly spaced hues which are then used to illustrate different taxa (default 'hls'). Note that this parameter only works if classification result was input.

General usage

1. ANI result visulization without classification info: $ pairwiseANIviz ani_result.txt

2. ANI result visulization with classification info: $ pairwiseANIviz aniresult.txt --classificationFile classificationresult.tsv

3. ANI result visualization with hierarchical clustering: $ pairwiseANIviz --rowCluster --colCluster ani_result.txt

Runjia Ji, 2023 ```

Citation

If you use pairwiseANIviz in your research, please cite our related paper:

Ji, R., Wan, J., Liu, J. et al. Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level. Microbiome 12, 158 (2024). https://doi.org/10.1186/s40168-024-01837-6

Contact

If you have any questions using pairwiseANIviz, feel free to open an issue or contact me jirunjia@gmail.com.