t test calculation tool for Pressure-Volume Loop (PVL) data

Python tool to perform an unpaired, two-sample student's t test on the mean values of Pressure-Volume Loop measurements (e.g., Heart rate (bpm), End-diastolic Volume (µL), Cardiac Output (µL/min)) for two groups (e.g., WildType vs Transgenic). Note: this tool has been designed to ingest Excel files with a specific format produced by a specific wet lab software (i.e., PVAN Ultra). See here for examples of the input files.

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Installation (Command Line Tool Only)

Use the package manager pip to install requirements.txt.

pip install -r requirements.txt

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Usage

The tool can be run as a web application (already deployed on the Streamlit Platform) or via the Command Line.

Web Application

To use the web application, click and perform the following:

• Type a group name (e.g., WildType) for Group 1.
• Upload all files for Group 1 (e.g., WT#1.xlsx, WT#2.xlsx, WT#3.xlsx)) for Group 1.
• Type a group name (e.g., Transgenic) for Group 2.
• Upload all files for Group 2 (e.g., TG#1.xlsx, TG#2.xlsx, TG#3.xlsx) for Group 2.
• Click Run Unpaired t test.
  • A bar chart comparing the p-val for each measurement will appear, to expand it hover over it and a set of arrows will appear on the right - click to expand. Click on the same arrows to return to the original view.
  • A table showing raw results from the test will also appear (expand in the same manner as above). These results can be download as a CSV by clicking on the download button. Note: that clicking on the button will cause the results to disappear from screen - this is due to Streamlit rerunning the whole application when it receives any input - click on Run Unpaired t test to reload the results.

Command Line Tool

To use the command line tool, perform the following:

• Create a folder for each group and store the relevant Excel files in each one, for example:

   C:\data
   +---Transgenic
   |		TG#1.xlsx
   |		TG#2.xlsx
   |		TG#3.xlsx
   +---WildType
   |		WT#1.xlsx
   |		WT#2.xlsx
   |		WT#3.xlsx

• Run the following command (on the command line):

   python run_t_test_cmd.py -i <input_dir> -o <output_dir> -g <group1,group2>

  Example:

   python run_t_test_cmd.py -i C:\data -o C:\results -g Transgenic,WildType

• The results will be saved to an Excel file named Group1_vs_Group2_DDMMYYYY_HHMI.xlsx in the output directory.