Title: Change from Baseline by Baseline: Categorical QTc Analysis

ClinECGVitalsGraphicsForm edit

Image	Click on hyperlink to see full graphic. 1 - Baseline QTc Hr 0 2 – Baseline QTc Hr 30 min 3 – Baseline QTc – 1 hr 4 – Baseline QTC Hr 2 5 – Baseline QTc Hr 3 6 – Baseline QTC Hr 4 7 – Baseline QTc Hr 6 8 – Baseline QTc Hr 9 9 – Baseline QTc Hr 12
Title	Change from Baseline by Baseline: Categorical QTc Analysis
Graph_Subgroup	ECGVitals
ECG_Vitals_Clinical_Question	2. Are there outlier individuals that have large changes or raw values?
Contributor/Email	Rich Anziano (richard.j.anziano@pfizer.com) Max Cherny (Max.2.Cherny@gsk.com)
Background	This figure plots the change from baseline by the baseline value and is useful in examination of 'categorical' QTc changes. By plotting the changes against the baseline one can view the changes in the context of the raw QTc values. Large changes toward the left hand side of the plot are most likely due to regression to the mean and a low baseline whereas large changes to the right-hand side of the plot have large raw QTc values as well as large changes and are potentially more worrisome. The plot presented here is produced by hour post dose in a throrough QT design and the 4 hour timepoint was presented as that represented tmax of the experimental drug.
Keywords	tqt, categorical qtc, baseline, change from baseline
References	http://www.fda.gov/downloads/RegulatoryInformation/Guidances/ucm129357.pdf Section 3.2.2
Datasets	Other
CDISC_Data
Other_Data	tQT Dataset and Description
CLASSIFICATIONS
Graph_Type	Scatterplot
Variable_Relationship	Continuous versus Continuous
Data_Types	Continuous
Special_Considerations
Code_Available	Yes
Software Program	R
Software
R-Code - Attachment	Cherny - R code - QTc Graphs
R-Code	#Contributed by Max Cherny (email: Max.2.Cherny@gsk.com) # clear objects rm(list = ls()) # close graphics windows graphics.off() #Need gridExtra for gridtext function require(gridExtra) #Read data. Make sure to specify path to the data file ecg <- read.table("tqt.dat", header=FALSE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) #create x, y, group and page variables ecg$tpd<-ecg$V3 ecg$y<-ecg$V20 ecg$x<-ecg$V8 #create numeric code variables for group ecg$groupcd<-as.numeric(ecg$V22) #create labels for groups ecg$group<- factor(ecg$groupcd, labels = c("Exp Low Dose", "Exp High Dose", "Placebo", "Moxifloxacin") ) #create short labels for groups ecg$groupt<- factor(ecg$groupcd, labels = c("l", "h", "p", "m") ) #keep only the required variables in dataset ecg<-ecg[c("x", "y", "groupcd", "tpd", "group", "groupt" )] #remove any records with missing data ecg<-na.omit(ecg) #check the ranges for x and y range(ecg$x,na.rm=TRUE) range(ecg$y,na.rm=TRUE) #create dataset containing unique TPD records unique_ecgs<-subset(ecg, duplicated(tpd)) #create variable representing row number for tpd variable. The counter will be used to create a graph per single page for (i in 1:nrow(unique_ecgs)) { unique_ecgs$tpdcd[i]=i } unique_ecgs<-unique_ecgs[,c('tpd', 'tpdcd')] #add tpd counter to ECG dataset ecg<-merge(ecg, unique_ecgs, by=c("tpd"), sort=T, all.y=T) #determine number of pages number_of_pages<- as.numeric(max(unique(ecg$tpdcd))) #determine number of treatments number_of_trt<- max(ecg$groupcd,na.rm=TRUE) # PDF file name. Add file path here somePDFPath = "ecg_vitals_G02.pdf" #direct output to PDF pdf(file=somePDFPath, paper='A4r', width=15, height=8) #set up margins par(new=T, par(mar=c(12,5,11,1))) #set up colors for each treatment colors<-c("cyan", "blue","red","black") #set up symbols for each treatment plotchar <-c(76,72,80,77) #77-M 76-L 72-H 80-P #plotchar <-c(108,104,112,109) #109 produces m as symbol, 108-l, 104 -h, 112-p. This code may be used for lower case letter symbols #Start a loop to create a graph per page for (ii in 1:number_of_pages) { #create a temporary dataset for per (i.e. the timepoint) ecg_temp1 <- subset(ecg, tpdcd==ii ) #create empty plot. The points will be added later plot( ecg_temp1$y~ecg_temp1$x, ylim = c(-60, 70) , #y-axis scale type="n", #supress plot yaxt = "n", xaxt="n", xlab="Baseline QTc (milliseconds) - Fridericia Correction", ylab=" QTc Change (milliseconds) - Fridericia Correction", xlim = c(350, 460) #x-axis scale ) #plot points for each treatment for (i in 1:number_of_trt) { #create temporary dataset for the treatment ecg_temp2 <- subset(ecg_temp1, groupcd==i ) #subset temp dataset #plot points points(ecg_temp2$x, ecg_temp2$y, cex=0.6, #size of points col=colors[i], #color of points pch=plotchar[i] #symbol of points ) } #end of (i in 1:number_of_trt) loop #legend legend("bottom" , inset=-0.5, #inset will display the legend below the plot xpd=T, as.character(unique(ecg$group)), #text for legend cex=1, col=colors, pch=plotchar, ncol=4, title="Treatments:") #this function is needed to determine the angle of reference line labes getCurrentAspect <- function() { uy <- diff(grconvertY(1:2,"user","inches")) ux <- diff(grconvertX(1:2,"user","inches")) uy/ux } asp <- getCurrentAspect(); #add reference lines abline (h=0, lty=2) abline (h=30, lty=2) abline (h=60, lty=2) #diagonal reference lines abline(a=450, b=-1, lty = 2) text(x=400, y=55, "450 msec", srt=180/piatan(-1asp)) abline(a=480, b=-1, lty = 2) text(x=430, y=55, "480 msec", srt=180/piatan(-1asp)) abline(a=500, b=-1, lty = 2) text(x=450, y=55, "500 msec", srt=180/piatan(-1asp)) #display x axis xaxis_marks <- seq(340,480,by=10) axis(1, tick=T, at=xaxis_marks,labels = T) #display y axis yaxis_marks <- seq(-70,80,by=10) axis(2, tick=T, at=yaxis_marks, las=2 ) #use las to display horizontal label on Y axis #add text at fixed positions grid.text(paste("user_id: ",toupper(format(Sys.time(), "%d%B%Y %H:%M"))), x=0.01, y=0.06,just="left") grid.text("Protocol: text", x=0.01, y=0.93,just="left") grid.text("Population: Text", x=0.01, y=0.9,just="left") grid.text( paste("Page", ii, "of", number_of_pages), x=0.9, y=0.9,just="left") grid.text(paste("ECG/VITALS G2"), x=0.5, y=0.88) grid.text("Figure Number", x=0.5, y=0.85) grid.text("Title2 (Base R)", x=0.5, y=0.82) grid.text( paste("Hour:", unique(ecg_temp2$tpd)),, x=0.5, y=0.75) } #end of (ii in 1:number_of_pages) loop dev.off()
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Other Code
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Topic revision: r8 - 01 May 2013 - 17:52:27 - MaryBanach

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