toolbox

Helpful python functions aggregated into one place

General helpers

• Functions that I tend to use a lot to make life easier

load_dataframe()

Infers what Pandas dataframe loader to use based on the file extension (or you can override), and returns the loaded dataframe.

partition_indexes()

Returns index positions to break up an iterable into chunks

upper_tri_index_unravel()

Get linear index of an upper triangle of a square matrix (nxn) while ignoring the main diagonal

upper_tri_index_ravel()

Get coordinates from a linear index of a square matrix while ignoring the main diagonal

etree_to_dict()

Makes a JSON-like dictionary from an xml file.

Mass Spectrometry helpers

• MetAtlas is an import, but is not required for most functions
• rdkit is an import, but is currently not required for any functions
• Most of these functions are designed to work with MetAtlas, Pactolus, or MAGI outputs

ppm_error()

Returns ppm error between two masses

ppm_window()

Returns mass-ppm and mass+ppm

find_mass()

Given a mass and ppm error, and optionally a retention time and window, gives you dataframe row(s) that have features that match your search

data_convert()

Converts a Pandas.Series object into dataframe for easier plotting

ctrl_expt_compare()

Removes peaks that were found in two samples

cpd_from_inchikey()

Uses MetAtlas database to get a compound object from an InChI-key

Matplotlib helpers

cmap_color()

Color maps one liner cmap example Notebook

subplot_row_col()

Makes plotting lots of subplots easy

calc_perp()

Calculates a point on a line perpendicular to an arbitrary point

twod_dist()

Calculates distance between two 2D points

elbow_point()

Finds the elbow point of an elbow plot

elbowpoint example Notebook

trendline()

Calculates a polynomial fit, optionally gives you confidence intervals for the polynomial

trendline example Notebook

stddev_from_trendline()

Calculates the linear regression of a 2D dataset, and gives you the vertical distance from the trendline that encompasses n-standard deviations of the data

trendline example Notebook

multivar_ellipse()

Draws an ellipse around multivariate data that encompasses n-sigma of the data

ellipse example Notebook