correlationReport: Correlation Report

In qfa: Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces

Description

Generates all possible fitness correlation plots, on a plate-by-plate basis, comparing all possible combinations of replicates for a given medium, treatment and plate number. Useful tool for searching for incorrect plate orientation, or misplaced/mislabelled plates. Can also give clues about plates with incorrect medium.

Usage

correlationReport(scrnms,dataframe,outputfile,aw=4,ah=4,fitmax=185,fdef="fit")

Arguments

dataframe	Dataframe containing fitnesses to be summarised. Typically output from qfa.fit function. Must add a "fit" column before passing to this function.
outputfile	Output file name.
scrnms	Screen names to test for correlation problems
fitmax	Upper limit for both x and y axes in correlation plots. Maximum observable fitness for this combination of experiments and fitness definitions.
aw	Number of horizontal panels per page in output report.
ah	Number of vertical panels per page in output report.
fdef	Fitness definition to use (e.g. "nAUC","r","MDR").

Value

Generates a multi-page .pdf report demonstrating two-way between-replicate correlation for all possible pairs of plates and for all media, treatments and replicates in a QFA experiment.

qfa documentation built on Feb. 22, 2020, 3:01 a.m.