GCPlot is a plotting software for growth curves with biological replicates. It works with experiments as growing cells under different conditions or growing different cells under the same conditions. Each of this differable varbiable, here, is called treatment. So, if one wants to compare growth of cells of the specie A under 37°C and 40°C, it’s said that there are two different treatments: 37°C and 40°C. It is the same if one wants to compare growth of cells of specie A and specie B under a fixed condition of 37°C; there are two different treatments: specie A and specie B.

Requirement

GCPlot only requires R and the package ggplot2

Usage

$ R -f GCPlot.R --args <growth_file.txt> <spec_file.spec> <plot_name.png> > stdout

For a cleaner status, set a standard output with > stdout

• growth_file.txt - A file containing the growth data tabular separated. Each row must have the growth estimation on each time, and the columns must correspond to the replicates.

The example bellow shows a file with columns corresponding to 2 different treatments with 3 replicates each;

time	treatment1 - replicate1	treatment1 - replicate2	treatment2 - replicate1	treatment2 - replicate2
0	0.5	0.5	0.5	0.5
1	0.6	0.6	0.5	0.5
…	…	…	…	…
180	2.1	2.4	0.7	0.9

This treatments can be either different strains of cells or even different environmental contitions. In the second case, it would look like follows:

time	condition1 - replicate1	condition1 - replicate2	condition2 - replicate1	condition2 - replicate2
0	0.5	0.5	0.5	0.5
1	0.6	0.6	0.5	0.5
…	…	…	…	…
180	2.1	2.4	0.7	0.9

For example, see gc_example_file.txt

• spec_file.spec A file containing information about the experiment. The lines must contain, basically, information to fill the output chart. The first two lines coresponds to X and Y label, respectively, and last one to the chart title. This file must be like follows:

Growth estimation method (OD, NCels..), default = OD600
Time units (hours, minutes ..), default = hours
Chart title, default = NULL

For example, see spec_example_file.spec

• plot_name.png Filename of the chart figure. It can be png, svg, jpg and all other formats supported by ggplot.