The bioinfokit toolkit aimed to provide various easy-to-use functionalities to analyze,
visualize, and interpret the biological data generated from genome-scale omics experiments.

<span style="color:#33a8ff">How to install:</span>

bioinfokit requires

Python 3
NumPy
scikit-learn
seaborn
pandas
matplotlib
SciPy
matplotlib_venn

bioinfokit can be installed using pip, easy_install and git.

latest bioinfokit version:

Install using <a href="https://pip.pypa.io/en/stable/installing/" target="_blank">pip</a> for Python 3 (easiest way)

# install
pip install bioinfokit

# upgrade to latest version
pip install bioinfokit --upgrade

# uninstall 
pip uninstall bioinfokit

Install using <a href="https://setuptools.readthedocs.io/en/latest/easy_install.html" target="_blank">easy_install</a> for Python 3 (easiest way)

# install latest version
easy_install bioinfokit

# specific version
easy_install bioinfokit==0.3

# uninstall 
pip uninstall bioinfokit

Install using <a href="https://docs.conda.io/en/latest/" target="_blank">conda</a>

conda install -c bioconda bioinfokit

Install using <a href="https://git-scm.com/book/en/v2/Getting-Started-Installing-Git" target="_blank">git</a>

# download and install bioinfokit (Tested on Linux, Mac, Windows) 
git clone https://github.com/reneshbedre/bioinfokit.git
cd bioinfokit
python setup.py install

Check the version of bioinfokit

>>> import bioinfokit
>>> bioinfokit.__version__
'0.4'

How to cite bioinfokit?

Renesh Bedre. (2020, March 5). reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit. Zenodo. http://doi.org/10.5281/zenodo.3698145.
Additionally check <a href='https://zenodo.org/record/3841708#.XyCfi-dOmUk' target='_blank'>Zenodo</a> to cite specific version of bioinfokit

Support

If you enjoy bioinfokit, consider supporting me,

Getting Started

Gene expression analysis

Volcano plot

latest update v2.0.8

bioinfokit.visuz.GeneExpression.volcano(df, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, dim, r, ar, dotsize, markerdot, sign_line, gstyle, show, figtype, axtickfontsize, axtickfontname, axlabelfontsize, axlabelfontname, axxlabel, axylabel, xlm, ylm, plotlegend, legendpos, figname, legendanchor, legendlabels, theme)

Parameters | 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 or list][default:(1.0, 1.0)] pv_thr | p value or adjusted p value cutoff for up and downregulated genes [Tuple or list][default:(0.05, 0.05)] color | Tuple of three colors [Tuple 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 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 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)

Parameters | Description ------------ | ------------- table |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values lfc | Name of a column having log fold change values [default:logFC] pv | Name of a column having P-values or adjusted P-values [default:p_values] lfc_thr | Log fold change cutoff for up and downregulated genes [Tuple or list] [default:(1.0, 1.0)] pv_thr | p value or adjusted p value cutoff for up and downregulated genes [Tuple or list] [default:(0.05, 0.05)] color | Tuple of three colors [Tuple 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 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] gstyle | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1] 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"] dim | Figure size [Tuple of two floats (width, height) in inches][default: (5, 5)] r | Figure resolution in dpi [int][default: 300]. Not compatible with show= True figtype | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] `s

Bioinfokit

Install / Use

README