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Title  Scatterplot w/ Density and Smoothed Regression 
Graph_Subgroup  General Principles 
Code Added  Yes 
Description  This is a scatterplot of efficacy counts at baseline versus counts at the end of treatment. It includes density estimates of the distributions at both baseline and end of treatment in the margins of the figure. Smoothed regression lines are provided within the scatterplot. 
Contributor/Email  Mat Soukup (email: Mat.Soukup@fda.hhs.gov) 
Background 
Efficacy comparison of two treatment groups where improvement is defined as a reduction in the count. The data set is a randomly generated data set (currently not provided). This type of plot allows one to see the bivariate relationship in the baseline and end of treatment counts for all subjets while also included a smoothed regression line which can be used as a way of assessing the treatment effect across all ranges of the baseline count. The densities provide a way to compare the distributions at baseline and end of treatment. 
Special Considerations 

Date  Original 
Original Date  2007 
Modified Date 

Use/Suitability  Publication 
Software Program  R 
Software 

RCode  Attachment  Scatter Plot Density 
RCode 
dat < read.csv('//cdsnas/oebdbdms/Graphics/DataSets/CleanTrial.csv') base < subset(dat, visit%in%2) eot < subset(dat, visit%in%6) rallx < range(base$count) rally < range(eot$count) lev < levels(base$trtf) coluer < c('blue','grey60') def.par < par(no.readonly = TRUE) # save default, for resetting... ctb < dat$count[dat$visit==2] cte < dat$count[dat$visit==6] ptrt < dat$trtf[dat$visit==2] lev < levels(ptrt) #png('C:/Research/Graphics/Graphs4Display/webpages/classes/pages/images/scatterdensity.png', # width=500, height=500) nf < layout(matrix(c(2,1,3,4),2,2,byrow=TRUE), c(3,1), c(1,3), TRUE) #layout.show(nf) #Add legend in upper right quadrant par(mar=c(0,0,0,0)) plot(1:10,1:10, axes=FALSE, type='n', xlab='',ylab='') points(1,7, col=coluer[1], pch=1, cex=1.5) points(1,4, col=coluer[2], pch=1, cex=1.5) text(1.1,7,'Active',col='blue', pos=4, cex=1.5) text(1.1,4,'Placebo',col='grey60', pos=4, cex=1.5) par(mar=c(0,4,1,1)) plot(c(min(ctb)1,max(ctb)+1),c(0,.02), type='n',axes=FALSE,xlab='',ylab='') dd < density(ctb[ptrt==lev[1]]) lines(dd$x, dd$y, col=coluer[1]) dd2 < density(ctb[ptrt==lev[2]]) lines(dd2$x, dd2$y, col=coluer[2]) par(mar=c(5,4,1,1)) plot(cte~ctb, type='n', xlab='Baseline Count', ylab='End of Treatment Count', xlim=c(min(ctb)1,max(ctb)+1), ylim=c(min(cte)1, max(cte)+1)) for(k in 1:length(lev)){ points(cte[ptrt==lev[k]]~ctb[ptrt==lev[k]], col=coluer[k], pch=1) plsmo(ctb[ptrt==lev[k]],cte[ptrt==lev[k]], add=TRUE, lty=1, col=coluer[k],lwd=2) } lines(c(10,200),c(10,200), lty=2, col='grey60') par(mar=c(5,0,1,1)) plot(c(0,0.02),c(min(cte)1,max(cte)+1), type='n',axes=FALSE,xlab='',ylab='') dd < density(cte[ptrt==lev[1]]) lines(dd$y, dd$x, col=coluer[1]) dd2 < density(cte[ptrt==lev[2]]) lines(dd2$y, dd2$x, col=coluer[2]) #dev.off() par(def.par) 
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Keywords  scatterplot, baseline count, end of treatment count, bivariate relationship 
OPTIONAL FIELDS 

References 
This graph essentially is just combining several basic plotting functions paying close attention to the par setting of mar. The location of each graph on the plotting region is controlled by using the layout function. An example of this type of graph is provided in the statistical review of NDA 50802 by Mat Soukup, Ph.D. 
Datasets 

Data 

Attached Data 

CATEGORIZATIONS 

ClassificationEvaluation  Efficacy 
ClassificationGraph Type  Scatterplot 
Graph_Type  Scatterplot 
Variable Relationship  Continuous versus Continuous 
Data Types  Continuous 
Special Cases 

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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