StatGraphTopic005 < CTSpedia

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The format is very good but continuous variables have been arbitrarily binned. The best display would preserve the continuous nature of all continuous variables.

-- FrankHarrell - 18 May 2016 %COMMENT%

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Image	%LIGHTBOX{ image="DotplotSOC.png" thumbnail = "tn_DotplotSOC.jpg" caption="Dotplot SOC"}% Click on image to enlarge.
Title	Dotplot of Primary SOC
Graph_Subgroup	General Principles
Code Added	Yes
Description	The following example is a dotplot of the percent of events occurring within a system organ classification for a single treatment group. The SOC are sorted according to the relative frequency.
Contributor/Email	Mat Soukup (email: Mat.Soukup@fda.hhs.gov) Sanjay Matange (email: Sanjay.Matange@sas.com)
Background
Special Considerations
Date	Original
Original Date	2007
Modified Date
Use/Suitability	Presentation
Software Program	R, SAS
Software	R version 2.10 SAS Version 9.40M3
R-Code - Attachment	R-script: Dotplot of Primary SOC
R-Code	library(lattice) set.seed(26) soc <- c('Infections and infestations',<br /> 'Neoplasms benign and malignant (incl. cysts and polyps)', 'Blood and the lymphatic system disorders', 'Immune system disorders', 'Endocrine disorders', 'Metabolism and nutrition disorders', 'Psychiatric disorders', 'Nervous system disorders', 'Eye disorders', 'Ear and labyrinth disorders', 'Cardiac disorders', 'Vascular disorders', 'Respiratory, thoracic and mediastinal disorders', 'Gastrointestinal disorders', 'Hepato-biliary disorders', 'Skin and subcutaneous tissue disorders', 'Musculoskeletal, connective tissue and bone disorders', 'Renal and urinary disorders', 'Pregnancy, puerperium and perinatal conditions', 'Reproductive system and breast disorders', 'Congenital and familial/genetic disorders', 'General disorders and administration site conditions', 'Investigations', 'Injury and poisoning', 'Surgical and medical procedures', 'Social circumstances') rate <- round(rnorm(length(soc), 8, 3), 1)<br />ratec <- as.character(rate)<br /># order by most frequent dat <- data.frame(soc, rate, ratec)<br /> sortmat <- function (Mat, Sort) { <br /> m <- do.call("order", as.data.frame(Mat[, Sort])) <br /> Mat[m, ] } sdat <- sortmat(dat, 2)<br /> # Set up the plot levpt <- unique(sdat$soc)<br /> npt <- length(levpt)<br /> png('C:/Research/Graphics/Graphs4Display/webpages/classes/pages/images/DotplotSOC.png', width=600, height=400) # Set-up Layout mylayout <- layout(matrix(c(1,2,3), byrow=TRUE, ncol=3),<br /> widths=c(4/10,1/10,5/10)) par(mar=c(5,1,2,0)) plot(x=c(0,max(nchar(as.character(sdat$soc)))+1), y=c(.9,npt+.1), ann=FALSE, axes=FALSE, type='n') title('System Organ Classification') text(x=rep(max(nchar(as.character(sdat$soc))), npt), y=1:npt, label=sdat$soc, adj=c(1,0.5)) par(mar=c(5,0,2,0)) plot(x=c(0,1), y=c(.9,npt+.1), ann=FALSE, axes=FALSE, type='n') title('%') text(x=rep(.5, npt), y=1:npt, label=sdat$ratec, adj=c(0.5,0.5)) par(mar=c(5,0,2,2)) plot(x=c(0,max(sdat$rate)+.25), y=c(.9,npt+.1), type='n', axes=FALSE, xlab='Relative Frequency of an Event (%)', ylab='', ylim=c(.9,npt+.1)) axis(1) #box() abline(v=c(0,5,10,15), col='grey80', lty=3, lwd=2) for(i in 1:npt){ lines(c(0,sdat$rate[i]),c(i,i), lty=1, col='grey60', lwd=2) } points(sdat$rate, 1:npt, pch=16, col='black', cex=2) dev.off()
SAS-Code - Attachment
SAS-Code	%let gpath='.'; %let dpi=200; ods html close; ods listing gpath=&gpath image_dpi=&dpi; /--Create data set--/ data dot; format Pct percent8.1; label pct='%'; label classification='System Organ Classification'; input Value Classification $6-65; Pct=Value/100; datalines; 1.6 Infections and infestations 11.4 Neoplasms benign and malignant (incl. cysts and polyps) 6.5 Blood and the lymphatic system disorders 10.5 Immune system disorders 6.8 Endocrine disorders 8.4 Metabolism and nutrition disorders 8.4 Psychiatric disorders 10.7 Nervous system disorders 7.9 Eye disorders 9.3 Ear and labyrinth disorders 12.8 Cardiac disorders 7.9 Vascular disorders 6.3 Respiratory, thoracic and mediastinal disorders 15.1 Gastrointestinal disorders 8.5 Hepato-biliary disorders 11.0 Skin and subcutaneous tissue disorders 8.1 Musculoskeletal, connective tissue and bone disorders 4.7 Renal and urinary disorders 2.8 Pregnancy, puerperium and perinatal conditions 10.4 Reproductive system and breast disorders 6.2 Congenital and familial/genetic disorders 9.3 General disorders and administration site conditions 15.7 Investigations 9.1 Injury and poisoning 8.8 Surgical and medical procedures 5.3 Social circumstances ; run; /--Sort by descending pct--/ proc sort data=dot out=dot_Sort; by descending pct; run; /--Create Dot Plot using SAS 9.40M3--/ ods graphics / reset width=5in height=3in imagename='Dotplot_of_Primary_SOC'; proc sgplot data=dot_sort noborder; dropline y=classification x=pct / dropto=y; scatter y=classification x=pct / markerattrs=(symbol=circlefilled); yaxistable classification pct / location=outside position=left pad=10 valuejustify=right valueattrs=(size=7) labelattrs=(size=8); xaxis min=0 grid offsetmin=0 label='Relative Frequency of an Event'; yaxis fitpolicy=none valueattrs=(size=7) reverse display=none; run;
Stata-Code - Attachment
Stata-Code
Other Code - Attachment
Other Code
Keywords	safety, events, system organ classification, treatment group
OPTIONAL FIELDS
References
Datasets
Data
Attached Data
CATEGORIZATIONS
Classification-Evaluation	Safety
Classification-Graph Type	Dotplot
Graph_Type	Dotplot
Variable Relationship	Continuous versus Categorical
Data Types	Categorical and 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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This topic: CTSpedia > WebHome > StatGraphHome > ContributeGraphics > StatGraphTopic005
Topic revision: 18 May 2016, FrankHarrell

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