generate_MIC_report: Generate a PDF with MIC raw results

In Vincent-AC/wellexplainer: Helper functions for MIC and Checkerboard experiments

Description

Generate a PDF with MIC raw results, with each plate and MIC results

Usage

generate_MIC_report(title, date, max.conc, data_file, species,
  negative_control_col = 12, positive_control_col = 11,
  highest_conc_col = 1, lowest_conc_col = 10, number_of_lines = 8,
  startRow = 24, endRow = 32, knit_root_dir = getwd(),
  output_dir = getwd())

Arguments

title	Title of the PDF file
max.conc	list of vector giving the maximum concentration of antibiotic used for each row of each plate. The first element of the list corresponds to the first excel sheet. The first element of each vector corresponds to the first line of the plates
data_file	Path to the output from the plate reader
negative_control_col	Number of the column that contains the negative control. Defaults to 12
positive_control_col	Number of the column that contains the positive control. Defaults to 11
lowest_conc_col	Number of the column that contains the lowest concentration of tested antibiotic. Defaults to 10
number_of_lines	Number of lines used by plate. Defaults to 8
knit_root_dir	Directory where the report should be knitted (using knitr) Defaults to the current working directory
output_dir	Directory where the PDF should be saved. Defaults to the current working directory

Examples

generate_MIC_report()

Vincent-AC/wellexplainer documentation built on May 28, 2019, 3:21 p.m.