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.anziano@pharmetheus.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/pi*atan(-1*asp)) abline(a=480, b=-1, lty = 2) text(x=430, y=55, "480 msec", srt=180/pi*atan(-1*asp)) abline(a=500, b=-1, lty = 2) text(x=450, y=55, "500 msec", srt=180/pi*atan(-1*asp)) #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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Disclaimer | The views expressed within CTSpedia are those of the author and must not be taken to represent policy or guidance on the behalf of any organization or institution with which the author is affiliated. |
Permission |
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT OLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
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