API

This Application Programming Interface (API) is the public interface for the objects and functions of our xOmics Python toolkit, which can be imported by:

import xomics as xo

You can then access all methods and objects via the xo alias, such as xo.load_dataset.

Data Handling

xomics.load_dataset([name, n, random, drop_na])	Loads protein benchmarking datasets.
xomics.PreProcess([col_id, col_name, str_quant])	Pre-processing class for quantifications of omics data.

Imputation

xomics.cImpute([col_id, col_name, str_quant])

Transparent hybrid data imputation method.

Ranking

xomics.pRank([col_id, col_name, str_quant])

Hybrid imputation algorithm for missing values (MVs) in (prote)omics data.

Integration

Mapping

Plotting

xomics.plot_volcano([ax, figsize, df, ...])	Generate and display a volcano plot based on fold-change and p-value data.
xomics.plot_imput_histo([ax, figsize, ...])	Plot histogram of raw and imputed data

Plot Utilities

xomics.plot_settings([font_scale, font, ...])	Configures general plot settings.
xomics.plot_legend([ax, dict_color, ...])	Sets an independntly customizable plot legend.
xomics.plot_get_clist([n_colors])	Returns list of 2 to 9 colors.
xomics.plot_gcfs([option])	Gets current font size (or axes linewdith).