Package: pairwiseANIviz
pairwiseANIvizPairwise ANI (Average Nucleotide Identity) visulization tool. This tool is suitable for visualizing the results of pairwise comparisons between multiple genomes.
pairwiseANIviz first usingScipyto perform hierarchical/agglomerative clustering, a clustermap is then generated usingSeabornwhich supports differentMatplotlibcolormaps.Main featuresSupport differentmatplotlib colormapsTaxonomic classification result can be included toillustrate different taxaSpecificoutrange ANI valuescan be set (eg. 95% ANI values)Multi-format outputs (JPG, PNG, TIFF, SVG, PDF, EPS)Example1. Using differentmatplotlib colormaps2. With taxonomy indicated by different palettes3. With ANI values illustrated4. With outrange ANI values (95%) colored redInstallation# Dependencies: Matplotlib, Seaborn, Scipy, Pandas# Install pairwiseANIviz using pippipinstallpairwiseANIviz==1.0UsageOptionsusage:pairwiseANIviz[options]anifile

positionalarguments:anifileFilecontainingpairwiseANIanalysisresult.

options:-h,--helpshowthishelpmessageandexit-v,--versionShowpairwiseANIvizversionnumberandexit.-oOUTDIR,--outdirOUTDIRDirectorytosavetheoutputfigures(default'pairwiseANIviz').--method{single,complete,average,weighted,centroid,median,ward}Linkagemethodtouseforcalculatingclusters(default'average').Seehttps://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}Thedistancemetrictouse(default'euclidean').Seehttps://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist-cmapCOLORMAP,--colormapCOLORMAPMatplotlibcolormapusedwhendrawingtheheatmapofANIvalues(default'Blues').Seehttps://matplotlib.org/stable/users/explain/colors/colormaps.html--figWidthFIGWIDTHFigurewidth(default'15').--figHeightFIGHEIGHTFigureheight(default'15').--linewidthLINEWIDTHLinewidthofthemainheatmap(default0.5)--linecolorLINECOLORLinecolorofthemainheatmap(default'grey').--rowClusterDrawtherowcluster.--colClusterDrawthecolumncluster.--annotationShowANIvaluesontheplot.--outrangeValueOUTRANGEVALUECellshaveANIvaluesoverspecificthresholdsettored(eg.cellshaveANIvalue>=0.95settored)(default100).-cCLASSIFICATIONFILE,--classificationFileCLASSIFICATIONFILEFilecontainingclassificationresultgeneratedbyGTDBTk(https://github.com/Ecogenomics/GTDBTk).-t{domain,phylum,class,order,family,genus,species},--taxaLevel{domain,phylum,class,order,family,genus,species}Taxalevelillustratedontheplot.Choosefrom"domain, phylum, class, order, family, genus, species".Notethatthisparameteronlyworksifclassificationresultwasinput.--colorPaletteCOLORPALETTEColorpaletteusedtoreturnaspecifiednumberofevenlyspacedhueswhicharethenusedtoillustratedifferenttaxa(default'hls').Notethatthisparameteronlyworksifclassificationresultwasinput.

Generalusage
----------------1.ANIresultvisulization**withoutclassificationinfo**:$pairwiseANIvizani_result.txt2.ANIresultvisulization**withclassificationinfo**:$pairwiseANIvizani_result.txt--classificationFileclassification_result.tsv

RunjiaJi,2023ContactIf you have any questions using AsperaSRAgetter, feel free to open an issue or contact mejirunjia@gmail.com.