1. A .Rmd R Markdown file that can be opened with RStudio and executed interactivelly from within Rstudio. (drc_script.Rmd)
2. A .R script that can be used from the terminal and will produce 2 pdf reports, one for each half of the plate (containing what is currently in the output folder of this repository). (process_csv_to_pdf.R) This script accepts a single .csv file as an input and can be used in the following way :
i) Make sure R is installed and in your path. To install R on Mac go here:
ii) From terminal, assuming that you are in DRC_neutralization/scripts (all paths are absolute) :
Rscript --vanilla process_csv_to_pdf.R <input_csv_path> <pdf_label> <output_folder>
3. A .R script that can be used from the terminal and will produce 2 pdf reports, one for each half of the plate. The script requires three parameters, the input folder,the output folder and the folder containing the csv files with the assay names to be used in the legend and tables. It generates two pdf reports (one for each half of the plate) in the output folder for ALL .csv files in the input folder (NOTE: if you have unrelated csvs in that folder the script will not work as it currently performs the same operation on ALL .csv files in the input folder). (process_csv_to_pdf_batch.R)
In addition, the script generates a master table of all assay attributes (ED50, SDR, etc) in the output folder that can be used to query across all experiments. (all paths are absolute)
Usage (assuming you are in the scripts folder):
Rscript --vanilla process_csv_to_pdf_batch.R <input_folder> <output_folder> <input_folder_for_legend_csvs>
Current assumptions for legend csv files: i) plate names are <input_csv_name>_legend.csv (example : LG128_Plate1_legend.csv), ii) assay names are in order going from the top of the plate to the bottom for each side of the plate (left or right).