cimcb-lite

cimcb lite

cimcb_lite is a lite version of the cimcb package containing a small number of basic tools for the statistical analysis of untargeted and targeted metabolomics data.

Installation

Dependencies

cimcb_lite requires:

• Python (>=3.5)
• Bokeh (>=1.0.0)
• NumPy
• SciPy
• scikit-learn
• Statsmodels
• tqdm

User installation

The recommend way to install cimcb_lite and dependencies is to using conda:

conda install -c cimcb cimcb_lite

or pip:

pip install cimcb_lite

Alternatively, to install directly from github:

pip install https://github.com/cimcb/cimcb_lite/archive/master.zip

API

For futher detail on the usage refer to the docstring.

cimcb_lite.model

• PLS_SIMPLS: Partial least-squares regression using the SIMPLS algorithm.
  • train: Fit the PLS model, save additional stats (as attributes) and return Y predicted values.
  • test: Calculate and return Y predicted value.
  • evaluate: Plots a figure containing a Violin plot, Distribution plot, ROC plot and Binary Metrics statistics.
  • calc_bootci: Calculates bootstrap confidence intervals based on bootlist.
  • plot_featureimportance: Plots feature importance metrics.
  • plot_permutation_test: Plots permutation test figures.

cimcb_lite.plot

• boxplot: Creates a boxplot using Bokeh.
• distribution: Creates a distribution plot using Bokeh.
• pca: Creates a PCA scores and loadings plot using Bokeh.
• permutation_test: Creates permutation test plots using Bokeh.
• roc_plot: Creates a rocplot using Bokeh.
• scatter: Creates a scatterplot using Bokeh.
• scatterCI: Creates a scatterCI plot using Bokeh.

cimcb_lite.cross_val

• kfold: Exhaustitive search over param_dict calculating binary metrics.

cimcb_lite.bootstrap

• Perc: Returns bootstrap confidence intervals using the percentile boostrap interval.
• BC: Returns bootstrap confidence intervals using the bias-corrected boostrap interval.
• BCA: Returns bootstrap confidence intervals using the bias-corrected and accelerated boostrap interval.

cimcb_lite.utils

• binary_metrics: Return a dict of binary stats with the following metrics: R2, auc, accuracy, precision, sensitivity, specificity, and F1 score.
• ci95_ellipse: Construct a 95% confidence ellipse using PCA.
• knnimpute: kNN missing value imputation using Euclidean distance.
• load_dataXL: Loads and validates the DataFile and PeakFile from an excel file.
• nested_getattr: getattr for nested attributes.
• scale: Scales x (which can include nans) with method: 'auto', 'pareto', 'vast', or 'level'.
• table_check: Error checking for DataTable and PeakTable (used in load_dataXL).
• univariate_2class: Creates a table of univariate statistics (2 class).
• wmean: Returns Weighted Mean. Ignores NaNs and handles infinite weights.

License

cimcb_lite is licensed under the MIT license.

Authors

• Kevin Mendez
• David Broadhurst

Correspondence

Professor David Broadhurst, Director of the Centre for Integrative Metabolomics & Computation Biology at Edith Cowan University.