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Scientific research data analysis tools

Project description

Overview

This package provides tools to analyze scientific research data, with a focus on plotting and statistical analysis. It is written in Python and was tested on Linux and MacOS.

Compatibility

This package is written in Python 3.6 and was tested on Linux and MacOS 13. It depends on the following libraries:

  • matplotlib 3.1.3
  • numpy 1.18.4
  • pandas 0.25.3
  • scipy 1.4.1

Installation

If you are new to installation of Python and its packages, a tutorial is on the Python’s website.

Installing Python libraries is most easily done with pip3, simply run in a terminal:

pip3 install --upgrade <library>

easy-data-analysis is packaged and available through PyPI, you can install it by running in a terminal:

pip3 install --upgrade easy-data-analysis

Source distributions are also available here on GitHub, download the source and install it by running:

pip3 install <path>

Command Line Interface

easy-data-analysis is accessible through a command line interface which follows this syntax:

eda <command> <subcommand> [arguments ...]

Type this in your terminal for more information:

eda --help

configure command

eda configure <subcommand>

configure manages the default arguments of all commands, i.e. the behaviour of commands when you do not provide optional arguments. Available subcommands:

  • spectrum: configure eda plot spectrum
  • kinetics: configure eda plot kinetics
  • default: rollback to the original configuration (the one provided when you install this package)

When you enter the configuration mode, instructions will be displayed before you are prompted for input. The name of the parameter is displayed followed by its current value between ( parentheses ).

You have three possible actions (validate any of them by pressing <Enter>):

  • keep the current value: leave the input field empty
  • modify the current value: type your input (if a list is expected, use space to separate values)
  • enter a void value (no value): enter ‘none’ (without quotes)

plot command

eda plot <subcommand> [arguments ...]

plot reads a CSV file and plots the data according to one of the following subcommands:

  • spectrum
  • kinetics

spectrum subcommand

This subcommand plots absorption spectra.

eda plot spectrum [arguments ...]

File names are positional arguments, they should be passed before optional argument. Optional arguments include:

  • -l or --label specify labels on data for the plot legend
  • --figure-size specify width and height in inches
  • --xcolumn name of the column containing x-axis values
  • --ycolumn name of the column containing y-axis values
  • --xlabel label on the plot’s x-axis
  • --ylabel label on the plot’s y-axis
  • --xlimit specify left and right values for x-axis limits
  • --ylimit specify bottom and top values for y-axis limits
  • --skip-header number of rows to skip at the beginning of the file
  • --legend-location run eda plot spectrum -h for more information
  • --title specify the title of the plot

For example:

eda plot spectrum file1.csv file2.csv -l experiment1 experiment2

For more information:

eda plot spectrum -h

kinetics subcommand

This subcommand plots absorption kinetics curves. It can also plot an exponential model curve fitted on the data. Parameters of the model will be printed on the console.

eda plot kinetics [arguments ...]

File names are positional arguments and should be passed before optional arguments. Optional arguments include:

  • -l or --label specify labels on data for the plot legend
  • -m or --model is a flag indicating an exponential model should be fitted on the data
  • --figure-size specify width and height in inches
  • --xcolumn name of the column containing x-axis values
  • --ycolumn name of the column containing y-axis values
  • --xlabel label on the plot’s x-axis
  • --ylabel label on the plot’s y-axis
  • --xlimit specify left and right values for x-axis limits
  • --ylimit specify bottom and top values for y-axis limits
  • --skip-header number of rows to skip at the beginning of the file
  • --legend-location run eda plot spectrum -h for more information
  • --title specify the title of the plot

For example:

eda plot kinetics file1.csv file2.csv -l experiment1 experiment2 -m

For more information:

eda plot kinetics -h

Project details


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