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TECAN-reader based yeast growth measurements in R

Installation

We recommend using this yaml file to create a dedicated Conda environment with all necessary dependencies (as explained below).

  1. Install the Conda package/environment management system (if you already have Conda skip to step 2):

    On MacOS, run:

    $ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ sh Miniconda3-latest-MacOSX-x86_64.sh

    On Linux, run:

    $ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh

    IMPORTANT: If in doubt, respond with "yes" to the following question during installation: "Do you wish the installer to initialize Miniconda3 by running conda init?". In this case Conda will modify your shell scripts (~/.bashrc or ~/.bash_profile) to initialize Miniconda3 on startup. Ensure that any future modifications to your $PATH variable in your shell scripts occur before this code to initialize Miniconda3.

  2. Clone the TECAN_analysis GitHub repository:

    $ git clone https://github.com/lehner-lab/TECAN_analysis.git

  3. Create the tecan Conda environment and activate it:

    $ conda env create -f TECAN_analysis/tecan.yaml
$ conda activate tecan

  4. Start an R session and install the growthrates package:

    > install.packages("growthrates")

Usage

$ conda activate tecan
$ TECAN_analysis/tecan.R -h
usage: tecan.R [--] [--help] [--opts OPTS] [--method METHOD]
       [--parameter PARAMETER] [--wells WELLS] [--deadThreshold
       DEADTHRESHOLD] [--lagThreshold LAGTHRESHOLD] [--outputPrefix
       OUTPUTPREFIX] [--designPath DESIGNPATH] [--plotWidth PLOTWIDTH]
       [--plotHeight PLOTHEIGHT] [--ODThreshold ODTHRESHOLD] excel_path

TECAN-reader based yeast growth measurements and summary plots

positional arguments:
  excel_path           Path to the Excel file

flags:
  -h, --help           show this help message and exit

optional arguments:
  -x, --opts           RDS file containing argument values
  -m, --method         Maximum growth rate method [default: heuristic]
  -p, --parameter      h-parameter; number of consecutive time points
                       to evaluate maximum growth rate [default: 15]
  -w, --wells          Comma-separated list of well ids [default: all]
  -d, --deadThreshold  Growth rate threshold for dead variants
                       [default: 0.05]
  -l, --lagThreshold   Lag time threshold (in hours) for problematic
                       variants [default: 48]
  -o, --outputPrefix   Output path prefix [default: no output file;
                       print results to stdout]
  --designPath         Path to the plain text file with 'Well',
                       'Plasmid' and 'Well class' columns [optional].
                       'Well' column is required whereas 'Plasmid' and
                       'Well class' columns are optional; valid 'Well
                       class' column values are: 'Sample', 'Positive
                       control', 'Negative control', 'Blank' and
                       'Discarded'; plasmid-specific growth curves are
                       produced if 'Plasmid' column is supplied;
                       plasmid-specific boxplots are produced if
                       'Plasmid' and 'Well class' columns are supplied.
  --plotWidth          Plot width in inches [default: 8]
  --plotHeight         Plot height in inches [default: 8]
  -O, --ODThreshold    Minimum optical density required to escape
                       'deadThreshold' [default: 0]

Demo

$ conda activate tecan
$ TECAN_analysis/tecan.R TECAN_analysis/TECAN_growths.xlsx

Dependencies

Requires the following R packages (see tecan.yaml):

  • readxl
  • growthrates
  • argparser
  • beeswarm
  • scales
  • data.table
  • ggplot2
  • reshape2

Although care has been taken to make the code distribution-independent, it is possible that some of the scripts only work on Unix/MacOS systems, and may need to be modified in order to run on Windows systems.