[R-gregmisc-commits] r2133 - in pkg/gplots: R man

[noreply at r-forge.r-project.org]

Author: warnes
Date: 2016-08-12 19:18:32 +0200 (Fri, 12 Aug 2016)
New Revision: 2133

Modified:
   pkg/gplots/R/plotmeans.R
   pkg/gplots/man/plotmeans.Rd
Log:
New parameter 'add' for plotmeans to allow *adding* means+confidence intervals to an existing plot.

Modified: pkg/gplots/R/plotmeans.R
===================================================================
--- pkg/gplots/R/plotmeans.R	2016-08-12 17:17:24 UTC (rev 2132)
+++ pkg/gplots/R/plotmeans.R	2016-08-12 17:18:32 UTC (rev 2133)
@@ -17,6 +17,7 @@
                         xaxt,
                         use.t = TRUE,
                         lwd=par("lwd"),
+                        add = FALSE,
                         ...)
 {
   if (invalid(formula) || (length(formula) != 3))
@@ -51,6 +52,7 @@
 
   if(!bars)
     {
+      if(add) par(new=TRUE)
       plot( means, ..., col=col, xlim=xlim)
     }
   else
@@ -77,7 +79,8 @@
 
       plotCI(x=1:length(means), y=means, uiw=ci.width, xaxt="n",
              xlab=xlab, ylab=ylab, labels=mean.labels, col=col, xlim=xlim,
-             lwd=barwidth, barcol=barcol, minbar=minbar, maxbar=maxbar, ... )
+             lwd=barwidth, barcol=barcol, minbar=minbar, maxbar=maxbar,
+             add=add, ... )
       if(invalid(xaxt) || xaxt!="n")
         axis(1, at = 1:length(means), labels = legends, ...)
 

Modified: pkg/gplots/man/plotmeans.Rd
===================================================================
--- pkg/gplots/man/plotmeans.Rd	2016-08-12 17:17:24 UTC (rev 2132)
+++ pkg/gplots/man/plotmeans.Rd	2016-08-12 17:18:32 UTC (rev 2133)
@@ -10,7 +10,7 @@
           digits=getOption("digits"), col="black", barwidth=1,
           barcol="blue", connect=TRUE, ccol=
           col, legends=names(means), xaxt, use.t=TRUE,
-          lwd=par("lwd"), ...)
+          lwd=par("lwd"), add = FALSE, ...)
 }
 \arguments{
   \item{formula}{symbolic expression specifying the outcome (continuous)
@@ -91,6 +91,9 @@
 
   \item{lwd}{Width of connecting lines  }
 
+  \item{add}{Logical specifying whether to add to an existing plot
+    (\code{add=TRUE}) or to generate a new plot (\code{add=FALSE}).}
+
   \item{\dots}{ optional plotting parameters. }
 
   }
@@ -133,7 +136,29 @@
                    "Ile-et-Vilaine Esophageal Cancer Study")
             )
   abline(v=c(6.5, 12.5, 18.5), lty=2)
+  grid()
 
+  # add to a boxplot
+  boxplot(ncases/ncontrols ~ interaction(agegp , alcgp, sep ="   "),
+          data=esoph,
+          xlab="Age Group and Alcohol Consumption",
+          ylab="# Cases / # Controls",
+          main=c("Fraction of Cases for by Age and Alcohol Consumption",
+                 "Ile-et-Vilaine Esophageal Cancer Study"),
+          ylim=c(-0.75, 1.5),
+          col="green"
+            )
+  plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep ="   "),
+            data=esoph,
+            connect=list(1:6,7:12,13:18,19:24),
+            barwidth=2,
+            barcol="dark blue",
+            col="dark blue",
+            add=TRUE)
+  grid()
+  abline(v=c(6.5, 12.5, 18.5), lty=2)
+
+
 }
 
 \author{Gregory R. Warnes \email{greg at warnes.net}}