/bioassay_plotting

R plotting for bioassays: fresh weight and disease index

Primary LanguageR

R plotting of bioassay data

This R script will take in a set of bioassay measurements in CSV format.

##Main directory provide a main directory which contains:

  1. /fw/ (csv files containing fresh weight measurements)
  2. /di/ (csv files containing disease index measurements from 0-4)
  3. optional: labels.csv which can overwrite the labels from the previously specified csv files.

The script will plot a 3x2 grid containing a row of freshweight average measurements and a row of stacked bargraphs containing the disease index measurements. The FW values were statistically evaluated for significance through a standard ANOVA and Tukey Honest Significant Difference (TukeyHSD) test. Labels (for example a, b, ab, c) were generated and plotted above the bar graph.

##Dependencies Due to many workarounds of formatting the data like we want for plotting, we need the following R libraries installed and imported:

  • library(ggplot2)
  • library(reshape2)
  • library(multcompView)
  • library(plyr)
  • library(tools)
  • library(gridExtra)
  • library(cowplot)
  • library(gdata)
  • library(dplyr)

##Sample output A sample output can be found here: sample_output.png