# pairwiseANIviz
[](https://badge.fury.io/py/pairwiseANIviz)
[](https://pepy.tech/project/pairwiseaniviz)
[](https://pepy.tech/project/pairwiseaniviz)
[](https://pepy.tech/project/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](https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage) is used to perform hierarchical/agglomerative clustering, followed by generating a clustermap using [Seaborn](https://seaborn.pydata.org/generated/seaborn.clustermap.html) that supports various [Matplotlib](https://matplotlib.org/stable/users/explain/colors/colormaps.html) 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)__
* __Automatic header detection__ for FastANI output files
* __Flexible input format__ support for various header styles
## Example
#### 1. Using different [matplotlib colormaps](https://matplotlib.org/stable/users/explain/colors/colormaps.html)
<img src="/static/example_with_diffferent_cmap.svg" alt="Figure"/>
#### 2. With taxonomy indicated by different palettes
<img src="/static/example_with_different_palette.svg" alt="Figure"/>
#### 3. With ANI values illustrated
<img src="/static/example_with_annotation.svg" alt="Figure"/>
#### 4. With outrange ANI values (95%) colored red
<img src="/static/example_with_outrangeValue.svg" alt="Figure"/>
## Installation
<!-- AsperaSRAgetter has been distributed on [pypi](https://pypi.org/project/AsperaSRAgetter/). You can easily install AsperaSRAgetter through pip. AsperaSRAgetter depends on Aspera-CLI to retrive sequencing data from ENA. It is recommended to install Aspera-CLI [with Conda](https://anaconda.org/hcc/aspera-cli). -->
```shell
# Dependencies: Matplotlib, Seaborn, Scipy, Pandas
# Install pairwiseANIviz using pip
pip install pairwiseANIviz==1.2
```
## 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 ani_result.txt --classificationFile classification_result.tsv
Runjia Ji, 2023
```
## Contact
If you have any questions using pairwiseANIviz, feel free to open an issue or contact me jirunjia@gmail.com.
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"description": "# pairwiseANIviz\n\n[](https://badge.fury.io/py/pairwiseANIviz)\n[](https://pepy.tech/project/pairwiseaniviz)\n[](https://pepy.tech/project/pairwiseaniviz)\n[](https://pepy.tech/project/pairwiseaniviz)\n\nPairwise ANI (Average Nucleotide Identity) visulization tool. This tool is designed to help visualize the results of pairwise comparisons among multiple genomes.\n\nFirst, [Scipy](https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage) is used to perform hierarchical/agglomerative clustering, followed by generating a clustermap using [Seaborn](https://seaborn.pydata.org/generated/seaborn.clustermap.html) that supports various [Matplotlib](https://matplotlib.org/stable/users/explain/colors/colormaps.html) colormaps.\n\n\n#### Main features\n* Support various __matplotlib colormaps__\n* Taxonomic classification result can be included to __illustrate different taxa__\n* Specific __outrange ANI values__ can be set (eg. 95% ANI values) \n* __Multi-format outputs (JPG, PNG, TIFF, SVG, PDF, EPS)__\n* __Automatic header detection__ for FastANI output files\n* __Flexible input format__ support for various header styles\n\n\n## Example\n#### 1. Using different [matplotlib colormaps](https://matplotlib.org/stable/users/explain/colors/colormaps.html)\n<img src=\"/static/example_with_diffferent_cmap.svg\" alt=\"Figure\"/>\n\n#### 2. With taxonomy indicated by different palettes\n<img src=\"/static/example_with_different_palette.svg\" alt=\"Figure\"/>\n\n#### 3. With ANI values illustrated\n<img src=\"/static/example_with_annotation.svg\" alt=\"Figure\"/>\n\n#### 4. With outrange ANI values (95%) colored red\n<img src=\"/static/example_with_outrangeValue.svg\" alt=\"Figure\"/>\n\n\n## Installation\n \n<!-- AsperaSRAgetter has been distributed on [pypi](https://pypi.org/project/AsperaSRAgetter/). You can easily install AsperaSRAgetter through pip. AsperaSRAgetter depends on Aspera-CLI to retrive sequencing data from ENA. It is recommended to install Aspera-CLI [with Conda](https://anaconda.org/hcc/aspera-cli). -->\n\n```shell\n# Dependencies: Matplotlib, Seaborn, Scipy, Pandas\n# Install pairwiseANIviz using pip\npip install pairwiseANIviz==1.2\n```\n\n\n\n\n## Usage\n\n\n \n\n#### Options\n\n```bash\nusage: pairwiseANIviz [options] anifile\n\npositional arguments:\n anifile File containing pairwise ANI analysis result.\n\noptions:\n -h, --help show this help message and exit\n -v, --version Show pairwiseANIviz version number and exit.\n -o OUTDIR, --outdir OUTDIR\n Directory to save the output figures (default 'pairwiseANIviz').\n --method {single,complete,average,weighted,centroid,median,ward}\n Linkage method to use for calculating clusters (default 'average').\n See https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage\n --metric {braycurtis,canberra,chebyshev,cityblock,correlation,cosine,dice,euclidean,hamming,jaccard,jensenshannon,kulczynski1,mahalanobis,matching,minkowski,rogerstanimoto,russellrao,seuclidean,sokalmichener,sokalsneath,sqeuclidean,yule}\n The distance metric to use (default 'euclidean').\n See https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist\n -cmap COLORMAP, --colormap COLORMAP\n Matplotlib colormap used when drawing the heatmap of ANI values (default 'Blues').\n See https://matplotlib.org/stable/users/explain/colors/colormaps.html\n --figWidth FIGWIDTH Figure width (default '15').\n --figHeight FIGHEIGHT\n Figure height (default '15').\n --linewidth LINEWIDTH\n Line width of the main heatmap (default 0.5)\n --linecolor LINECOLOR\n Line color of the main heatmap (default 'grey').\n --rowCluster Draw the row cluster.\n --colCluster Draw the column cluster.\n --annotation Show ANI values on the plot.\n --outrangeValue OUTRANGEVALUE\n Cells have ANI values over specific threshold set to red (eg. cells have ANI value >=0.95 set to red) (default 100).\n -c CLASSIFICATIONFILE, --classificationFile CLASSIFICATIONFILE\n File containing classification result generated by GTDBTk(https://github.com/Ecogenomics/GTDBTk).\n -t {domain,phylum,class,order,family,genus,species}, --taxaLevel {domain,phylum,class,order,family,genus,species}\n Taxa level illustrated on the plot.\n Choose from \"domain, phylum, class, order, family, genus, species\".\n Note that this parameter only works if classification result was input.\n --colorPalette COLORPALETTE\n Color palette used to return a specified number of evenly spaced hues which are then used to illustrate different taxa (default 'hls').\n Note that this parameter only works if classification result was input.\n\nGeneral usage\n----------------\n1. ANI result visulization **without classification info**:\n $ pairwiseANIviz ani_result.txt\n\n2. ANI result visulization **with classification info**:\n $ pairwiseANIviz ani_result.txt --classificationFile classification_result.tsv\n\nRunjia Ji, 2023\n\n```\n\n## Contact\nIf you have any questions using pairwiseANIviz, feel free to open an issue or contact me jirunjia@gmail.com.\n",
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