plotPDF: Routine to generate PDF plots using the Diversity Assay Analysis Tool

Description

plotPDF uses various passed input, output and analysis parameters for performing an analysis on the data from an HIV Diversity Assay. The data consists of fluorescence measures, the analysis identifies candidate melting temperatures, peak changes in fluorescence and other statistics as they relate to the data. A PDF showing the fluorescence and dFluorescence curves together with the identified points for T1, T2 and Tm is generated for each sample. Parameters are listed below (default values are in parenthesis).

Usage

plotPDF(dir,
	singleFile,
	selectList,
	sampleMask,
	theta1=50,
	theta2=30,
	excludeEarly,
	earlyCutoff,
	excludeLate,
	lateCutoff,
	includeShoulders,
	shoulderCutoff,
	t1Cutoff,
	t2Cutoff,
	t1SlopeWindow,
	t2SlopeWindow,
	scoreFile,
	showFlorSmooth,
	showDFlorSmooth,
	useLasso,
	modelFile,
	xrangeOverride,
	xrangemin,
	xrangemax,
	rejectsFile,
	statsFile,
	progressFunc)

Arguments

dir

directory containing desired ABT/FLO files (required)

singleFile

a single file in that directory (for just one file)

selectList

a list of samples to plot (searched for in the file or files above), the default is to do all

sampleMask

a full or partial sample name or regular expression used to select individual samples

theta1

T1 cutoff angle (50 deg)

theta2

T2 cutoff angle as absolute value (30 deg)

excludeEarly

exclude peaks before main peak (T)

earlyCutoff

spacing required for exclusion (3 deg C)

excludeLate

exclude peaks after main peak (F)

lateCutoff

spacing required for exclusion (3 deg C)

includeShoulders

include premature shoulders in rising curve (T)

shoulderCutoff

fractional height at which to start inclusion (0.1)

showFlorSmooth

flag to enable drawing of smoothing curve for Florescence plot (F)

showDFlorSmooth

flag to enable drawing of smoothing curve for dFlorescence plot (T)

useLasso

flag to indicate whether to use regression model to filter bad data files (T)

t1Cutoff

delta temp that Theta 1 must be exceeded for T1 candidates (1 deg C)

t2Cutoff

delta temp that Theta 2 must be exceeded for T2 candidates (1 deg C)

t1SlopeWindow

Interval used to approximate slope at T1 (1 deg C)

t2SlopeWindow

Interval used to approximate slope at T2 (1 deg C)

scoreFile

DivMelt score file to compare against

modelFile

Alternate Lasso model file saved as an R object

rejectsFile

File to which to write names of Lasso rejected samples ("rejected.csv")

statsFile

File to which to write statistics like mean, max, etc. - used to help make a Lasso model training set

xrangeOverride

Option to override x-axis range (FALSE)

xrangemin

Value to use as override to x-axis min (75)

xrangemax

Value to use as override to x-axis min (100)

progressFunc

Optional function to call during processing passing it the fraction complete as a real