Summarize & Plot

Table of Contents


AMiGA can summarize and plot a 96-well plate


Let us assume that my working directory is

/Users/firasmidani/experiment


and I stored my plate reader file in the data sub-folder

/Users/firasmidani/experiment/data/ER1_PM2-1.txt


First, make sure that you are inside the AMiGA directory

cd /Users/firasmidani/amiga


Second, if you simply would like to plot the raw data in a 96-well grid, you can run the following:

python amiga.py summarize -i /Users/firasmidani/experiment/data/ER1_PM2-1.txt
  • summarize tells AMiGA to plot the plate, summarize basic metrics of each curve, and save both.
  • -i or --input argument will point to the location of the file of interest


Typical plot output

In your /Users/firasmidani/experiment/figures folder, you will find ER1_PM2-1.pdf.



example_96_well_plot



This example shows a Biolog PM2 plate where the A1 well is a negative control well (no carbon substrate). AMiGA computed the fold-change for all wells relative to the negative control well. Fold-change is computed as maximum change in OD in each well relative to the first time point divided by the maximum change in OD in the control well relative to the first time point. The numbers on the top right of each plot is the raw maximum OD in each curve. AMiGA highlighted wells where the fold-change is higher than 1.5 in blue or lower than 0.5 in red. If you want to change the default values for these thresholds, choice of colors, or y-axis label, you can make changes these parameters in libs/config.py file (see Configure default parameters). Color highlighting is only applicable if



Typical summary output

In addition to the plot, AMiGA summarizes the following basic metrics for all growth curves and records these metrics as tables in the summary folder where you will find ER1_PM2-1.txt.

Metric Description
OD_Baseline The OD measurement at the first time point
OD_Min The minimum OD measurement at any time point
OD_Max The maximum OD measurement at any time point
Fold_Change defined as the ratio of change in OD of the case (or treatment) growth curve relative to change in OD of the control growth curve


Here, fold change is mathematically defined as

\[\text{Fold Change} = \frac{ \displaystyle \max \text{OD}_{\text{case}}(t)- \text{OD}_{\text{case}}(0)}{ \displaystyle \max \text{OD}_{\text{control}}(t) - \text{OD}_{\text{control}}(0)} \quad \text{where} \quad\]


How to summarize multiple 96-well plates with a single command?

This is super easy. Just point AMiGA to the working directory instead of an individual file. AMiGA will find all of the data files, plot them, and save the figures as PDFs in the figures folder, and save summary tables in the summary folder.

python amiga.py summarize -i /Users/firasmidani/experiment


If you would like one single summary file for multiple plates, you should include the --merge-summary argument and also add the -o argument for naming the output file.

python amiga.py summarize -i /Users/firasmidani/experiment --merge-summary -o all_summary_tables

This will save a single summary file named all_summary_tables_basic.txt. If you do not pass an -o argument, AMiGA will name the file using a unique time stamp.