plotAllABT {AntibodyTiters}

Plotting antibody titers of All patients.

Description

This function plots antibody titers of all the patients in the ABT class object produced by readABT.

Usage

plotAllABT(objName = "inData", prefix = "", 
    dayStart = as.integer(NA), dayEnd = as.integer(NA), 
    type = "weeks", rainbow = FALSE, ylab = "Titer (AU/ml)", savePDF = FALSE, 
    alphaFactor = 10, lwd = 2, lineAttrib = "", addPoints = FALSE, 
    orderOfCategories = "", lowessSmooth = FALSE, geometricMean = FALSE,
    lineForPre = FALSE, lineFor1st = FALSE, logY = TRUE, PDFwidth = 8, PDFheight = 5, 
    main = NULL, omitPreVac = FALSE, lineColDark = FALSE)

Arguments

objName

a character specifying the name of an ABT class object produced by readABT.

prefix

a character to be atattched to the file name. This is active when savePDF==TRUE.

dayStart

an integer specifying the start day, from which scores are plotted.

dayEnd

an integer specifying the end day, to which scores are plotted.

type

a character determining the time scale; "weeks", "days", "M1", "M2", "M3", "M4", "M6". When "weeks" or "days" is chosen, plotting will be done on a continuous time scale. In contrast, when "M1" or other "M-" is chosen, time scale will be discrete. Bin sizes are one month (M1), two (M2), three (M3), four (M4), and six (M6) months.

rainbow

a logical indicating wether the line color is rainbow.

ylab

a character for the y-axix label.

savePDF

a logical indicating wether a PDF file is stored in the current directory.

alphaFactor

an integer for controlling the transparency of lines.

lwd

an integer for controlling the width of lines.

lineAttrib

a character specifying the name of attribute for which lowess or geometric mean lines are drawn for each group.

addPoints

a logical indicating wether points are plotted. This is active when lineAttrib!="".

orderOfCategories

a character vector specifying the order of categories listed as legends. This is active when lineAttrib!="".

lowessSmooth

a logical indicating wether lowess lines are plotted. This is active when lineAttrib!="".

geometricMean

a logical indicating wether geometric mean lines are plotted. This is active when lineAttrib!="".

lineForPre

a logical indicating wether lines that connects the pre-vaccination sampling point to others are plotted. This is active when lineAttrib!="" & geometricMean==TRUE.

lineFor1st

a logical indicating wether lines that connects the after-1st shot sampling point to others are plotted. This is active when lineAttrib!="" & geometricMean==TRUE.

logY

a logical indicating whether Y-axis is in log scale.

PDFwidth

an integer specifying the width of PDF. This is active when savePDF==TRUE.

PDFheight

an integer specifying the height of PDF. This is active when savePDF==TRUE.

main

a character for the main title. When not specified, objName will be used as the title.

omitPreVac

a logical indicating whether pre-vaccination will be omitted.

lineColDark

a logical indicating whether line colors will be darkened.

Value

No object will be returned. Instead, this function will drow a plot in a graphic device, or save a PDF file in the current directory.

Examples

inData <- readABT(fileName = system.file("extdata","toy.xlsx",package="AntibodyTiters"))

# logY
plotAllABT(objName = "inData", type = "weeks", rainbow = TRUE, logY = TRUE)
plotAllABT(objName = "inData", type = "weeks", rainbow = TRUE, logY = FALSE)

# lineAttrib, lowessSmooth, addPoints
plotAllABT(objName = "inData", type = "weeks", rainbow = FALSE, 
    lineAttrib = "Sex")
plotAllABT(objName = "inData", type = "weeks", rainbow = FALSE, 
    lineAttrib = "Sex", lowessSmooth = TRUE)
plotAllABT(objName = "inData", type = "weeks", rainbow = FALSE, 
    lineAttrib = "Sex", lowessSmooth = TRUE, addPoints = TRUE)
plotAllABT(objName = "inData", type = "weeks", rainbow = FALSE, 
    lineAttrib = "VeryLow", lowessSmooth = TRUE, addPoints = TRUE)
    
# Discrete mode, geometricMean
plotAllABT(objName = "inData", 
    type = "M1", lineAttrib = "Sex", geometricMean = TRUE)
plotAllABT(objName = "inData", 
    type = "M3", lineAttrib = "Sex", geometricMean = TRUE)

# alphaFactor, lwd
plotAllABT(objName = "inData", type = "weeks", rainbow = TRUE)
plotAllABT(objName = "inData", type = "weeks", rainbow = TRUE, alphaFactor = 20)
plotAllABT(objName = "inData", type = "weeks", rainbow = TRUE, lwd = 4)

# dayStart, dayEnd
plotAllABT(objName = "inData", dayStart = as.integer(NA), dayEnd = as.integer(NA), 
    type = "weeks", rainbow = TRUE)
plotAllABT(objName = "inData", dayStart = 140, dayEnd = 350, 
    type = "weeks", rainbow = TRUE)
plotAllABT(objName = "inData", dayStart = 140, dayEnd = 350, 
    type = "days", rainbow = TRUE)

# orderOfCategories, lowessSmooth
inDataA <- groupAttribABT(objName = "inData")
plotAllABT(objName = "inDataA", 
    type = "weeks", lineAttrib = "AgeGroup", addPoints = TRUE, lowessSmooth = TRUE)
plotAllABT(objName = "inDataA", 
    type = "weeks", lineAttrib = "AgeGroup", addPoints = TRUE, lowessSmooth = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"))

# lineForPre, lineFor1st
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = FALSE, lineFor1st = FALSE)
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = TRUE, lineFor1st = TRUE)
    
# omitPreVac (type = "days")
plotAllABT(objName = "inDataA", 
    type = "days", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), omitPreVac = FALSE)
plotAllABT(objName = "inDataA", 
    type = "days", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), omitPreVac = TRUE)
    
# omitPreVac (type = "M1")
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = TRUE, lineFor1st = TRUE, omitPreVac = FALSE)
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = FALSE, lineFor1st = TRUE, omitPreVac = TRUE)
    
# lineColDark (type = "days")
plotAllABT(objName = "inDataA", 
    type = "days", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), lineColDark = FALSE)
plotAllABT(objName = "inDataA", 
    type = "days", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), lineColDark = TRUE)
    
# lineColDark (type = "M1")
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = TRUE, lineFor1st = TRUE, lineColDark = FALSE)
plotAllABT(objName = "inDataA", 
    type = "M1", lineAttrib = "AgeGroup", addPoints = TRUE, 
    orderOfCategories = c("young", "middle", "elderly"), geometricMean = TRUE, 
    lineForPre = TRUE, lineFor1st = TRUE, lineColDark = TRUE)