Pairwise ANI (Average Nucleotide Identity) visulization tool.
Project description
pairwiseANIviz
Pairwise ANI (Average Nucleotide Identity) visulization tool. This tool is suitable for visualizing the results of pairwise comparisons between multiple genomes. pairwiseANIviz first using Scipy to perform hierarchical/agglomerative clustering, a clustermap is then generated using Seaborn which supports different Matplotlib colormaps.
Main features
- Support different 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==1.0
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
2. ANI result visulization **with classification info**:
$ pairwiseANIviz ani_result.txt --classificationFile classification_result.tsv
Runjia Ji, 2023
Contact
If you have any questions using AsperaSRAgetter, feel free to open an issue or contact me jirunjia@gmail.com.
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