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%global _empty_manifest_terminate_build 0
Name: python-bioinfokit
Version: 2.1.0
Release: 1
Summary: Bioinformatics data analysis and visualization toolkit
License: MIT
URL: https://github.com/reneshbedre/bioinfokit
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/19/2d/4fb9189fcd7d3018aeec6b1940485e90d4c69a30e95b2bdf0405c565cecb/bioinfokit-2.1.0.tar.gz
BuildArch: noarch
%description
`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns
`lfc` | Name of a column having log or absolute fold change values [string][default:logFC]
`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values]
`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)]
`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)]
`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")]
`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0]
`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None]
`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None]
`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2.
`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)]
`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True
`ar` | Rotation of X and Y-axis ticks labels [float][default: 90]
`dotsize`| The size of the dots in the plot [float][default: 8]
`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"]
`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False]
`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1]
`show` | Show the figure on console instead of saving in current folder [True or False][default:False]
`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png']
`axtickfontsize` | Font size for axis ticks [float][default: 9]
`axtickfontname` | Font name for axis ticks [string][default: 'Arial']
`axlabelfontsize` | Font size for axis labels [float][default: 9]
`axlabelfontname` | Font name for axis labels [string][default: 'Arial']
`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None]
`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None]
`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None]
`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None]
`plotlegend` | plot legend on volcano plot [True or False][default:False]
`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"]
`figname` | name of figure [string ][default:"volcano"]
`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None]
`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']]
`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None']
Returns:
Volcano plot image in same directory (volcano.png)
<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a>
### Inverted Volcano plot
latest update v2.0.8
`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle,
dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize,
axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)`
%package -n python3-bioinfokit
Summary: Bioinformatics data analysis and visualization toolkit
Provides: python-bioinfokit
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-bioinfokit
`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns
`lfc` | Name of a column having log or absolute fold change values [string][default:logFC]
`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values]
`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)]
`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)]
`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")]
`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0]
`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None]
`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None]
`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2.
`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)]
`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True
`ar` | Rotation of X and Y-axis ticks labels [float][default: 90]
`dotsize`| The size of the dots in the plot [float][default: 8]
`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"]
`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False]
`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1]
`show` | Show the figure on console instead of saving in current folder [True or False][default:False]
`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png']
`axtickfontsize` | Font size for axis ticks [float][default: 9]
`axtickfontname` | Font name for axis ticks [string][default: 'Arial']
`axlabelfontsize` | Font size for axis labels [float][default: 9]
`axlabelfontname` | Font name for axis labels [string][default: 'Arial']
`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None]
`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None]
`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None]
`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None]
`plotlegend` | plot legend on volcano plot [True or False][default:False]
`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"]
`figname` | name of figure [string ][default:"volcano"]
`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None]
`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']]
`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None']
Returns:
Volcano plot image in same directory (volcano.png)
<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a>
### Inverted Volcano plot
latest update v2.0.8
`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle,
dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize,
axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)`
%package help
Summary: Development documents and examples for bioinfokit
Provides: python3-bioinfokit-doc
%description help
`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns
`lfc` | Name of a column having log or absolute fold change values [string][default:logFC]
`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values]
`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)]
`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)]
`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")]
`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0]
`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None]
`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None]
`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2.
`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)]
`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True
`ar` | Rotation of X and Y-axis ticks labels [float][default: 90]
`dotsize`| The size of the dots in the plot [float][default: 8]
`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"]
`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False]
`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1]
`show` | Show the figure on console instead of saving in current folder [True or False][default:False]
`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png']
`axtickfontsize` | Font size for axis ticks [float][default: 9]
`axtickfontname` | Font name for axis ticks [string][default: 'Arial']
`axlabelfontsize` | Font size for axis labels [float][default: 9]
`axlabelfontname` | Font name for axis labels [string][default: 'Arial']
`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None]
`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None]
`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None]
`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None]
`plotlegend` | plot legend on volcano plot [True or False][default:False]
`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"]
`figname` | name of figure [string ][default:"volcano"]
`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None]
`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']]
`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None']
Returns:
Volcano plot image in same directory (volcano.png)
<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a>
### Inverted Volcano plot
latest update v2.0.8
`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle,
dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize,
axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)`
%prep
%autosetup -n bioinfokit-2.1.0
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-bioinfokit -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 2.1.0-1
- Package Spec generated
|
