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

# Dependencies: Matplotlib, Seaborn, Scipy, Pandas
# Install pairwiseANIviz using pip
pip install pairwiseANIviz==1.3

Usage

Options

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 --rowCluster --colCluster

2. ANI result visulization **with classification info**:
   $ pairwiseANIviz ani_result.txt --classificationFile classification_result.tsv --rowCluster --colCluster

Runjia Ji, 2023

Example usage

Suppose you have a txt file (genome_list.txt) contain a list of genomes/MAGs waiting for pairwise comparison, each line is a genome/MAG.

You can choose either fastANI or skani for the pairwise ANI calculation.

Option1. Use fastANI

fastANI --ql genome_list.txt --rl genome_list.txt -t 2 -o ani_result.txt

Option2. Use skani

skani dist --ql genome_list.txt --rl genome_list.txt -t 2 -o ani_result.txt

Then simply run:

pairwiseANIviz ani_result.txt --rowCluster --colCluster

You can adjust the linewidth, colormap, figuresize, wheather to show the x/y labels etc. based on the visualization results. Note that if you don't assign a new output folder, everytime you run it will rewrite the default output.

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.