[Analogue-commits] r160 - in pkg: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 2 16:47:59 CET 2010
Author: gsimpson
Date: 2010-03-02 16:47:59 +0100 (Tue, 02 Mar 2010)
New Revision: 160
Modified:
pkg/R/plot.roc.R
pkg/inst/ChangeLog
pkg/man/plot.roc.Rd
Log:
add more flexible handling of line types in plot.roc
Modified: pkg/R/plot.roc.R
===================================================================
--- pkg/R/plot.roc.R 2010-03-02 08:30:14 UTC (rev 159)
+++ pkg/R/plot.roc.R 2010-03-02 15:47:59 UTC (rev 160)
@@ -6,6 +6,7 @@
abline.col = "grey",
inGroup.col = "red",
outGroup.col = "blue",
+ lty = "solid",
caption = c("ROC curve",
"Dissimilarity profiles",
"TPF - FPF vs Dissimilarity",
@@ -34,12 +35,15 @@
}
}
method <- attr(x, "method")
+ ## replicate lty if length 1
+ if(length(lty) == 1L)
+ lty <- rep(lty, 2)
if(show[1]) {
plot(x$roc[[group]]$FPE, x$roc[[group]]$TPF, type = "n",
ylab = "TPF (sensitivity)",
xlab = "1 - TNF (1 - specificity)")
abline(0, 1, col = abline.col)
- lines(x$roc[[group]]$FPE, x$roc[[group]]$TPF, ...)
+ lines(x$roc[[group]]$FPE, x$roc[[group]]$TPF, lty = lty[1L], ...)
mtext(caption[1], side = 3, line = 1.7, font = 2)
if(show.stats) {
txt <- paste("AUC =", round(x$roc[[group]]$AUC, 3))
@@ -62,8 +66,8 @@
xlab = paste("Dissimilarity (", attr(x, "method"), ")",
sep = ""))
abline(h = 0, col = abline.col)
- lines(dens.in, col = inGroup.col)
- lines(dens.out, col = outGroup.col)
+ lines(dens.in, col = inGroup.col, lty = lty[1L], ...)
+ lines(dens.out, col = outGroup.col, lty = lty[2L], ...)
abline(v = x$roc[[group]]$optimal, lty = "dotted",
col = abline.col)
axis(side = 2)
@@ -72,9 +76,9 @@
mtext(caption[2], side = 3, line = 1.7, font = 2)
legend("topright", legend = c("Analogue", "Not Analogue"),
col = c(inGroup.col, outGroup.col),
- lty = "solid", lwd = 1,
+ lty = lty[c(1L,2L)],
bty = "n", cex = 0.8,
- inset = 0.01)
+ inset = 0.01, ...)
}
if(show[3]) {
cutpoints <- unique(rev(x$roc[[group]]$roc.points))
@@ -84,7 +88,7 @@
xlab = paste("Dissimilarity (", attr(x, "method"), ")",
sep = ""))
abline(h = 0, col = abline.col)
- lines(cutpoints, roc.values)
+ lines(cutpoints, roc.values, lty = lty[1L], ...)
abline(v = x$roc[[group]]$optimal, lty = "dotted",
col = abline.col)
mtext(caption[3], side = 3, line = 1.7, font = 2)
@@ -99,7 +103,7 @@
sep = ""))
abline(v = x$roc[[group]]$optimal, lty = "dotted",
col = abline.col)
- lines(dissims, pos, col = inGroup.col)
+ lines(dissims, pos, col = inGroup.col, lty = lty[1L], ...)
axis(side = 1)
axis(side = 2)
usr <- par("usr")
@@ -108,22 +112,22 @@
min(neg[finite.vals])) * 0.04
par(usr = c(usr[1:2], min(neg[finite.vals]) - rany,
max(neg[finite.vals]) + rany))
- lines(dissims, neg, col = outGroup.col)
+ lines(dissims, neg, col = outGroup.col, lty = lty[2L], ...)
axis(side = 4)
box()
mtext(caption[4], side = 3, line = 1.7, font = 2)
legend("topright", legend = c("LR (+)", "LR (-)"),
col = c(inGroup.col, outGroup.col),
- lty = "solid", lwd = 1,
+ lty = lty,
bty = "n", cex = 0.8,
- inset = 0.01)
+ inset = 0.01, ...)
}
if(show[5]) {
plot(l.ratios, group = group,
abline.col = abline.col, col = inGroup.col,
ylab = "Pr (A+ | d)",
xlab = paste("Dissimilarity (", attr(x, "method"), ")",
- sep = ""))
+ sep = ""), lty = lty[1L], ...)
##mtext(caption[5], side = 3, line = 1.7, font = 2)
}
invisible()
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2010-03-02 08:30:14 UTC (rev 159)
+++ pkg/inst/ChangeLog 2010-03-02 15:47:59 UTC (rev 160)
@@ -19,6 +19,10 @@
statistics. Fixed to use the points established by 'table', used to
generate these other statistics. This affected the plot method.
+ * plot.roc: Allow user to specify the line types used to draw the
+ plots. Two line types can be specified for plots comparing analogue
+ with non-analogue statistics.
+
Version 0.6-22
* tran.formula: bug in my implementation of the standard
Modified: pkg/man/plot.roc.Rd
===================================================================
--- pkg/man/plot.roc.Rd 2010-03-02 08:30:14 UTC (rev 159)
+++ pkg/man/plot.roc.Rd 2010-03-02 15:47:59 UTC (rev 160)
@@ -18,6 +18,7 @@
abline.col = "grey",
inGroup.col = "red",
outGroup.col = "blue",
+ lty = "solid",
caption = c("ROC curve", "Dissimilarity profiles",
"TPF - FPF vs Dissimilarity",
"Likelihood ratios"),
@@ -48,6 +49,13 @@
\item{outGroup.col}{character string or numeric value; the colour used
to draw the density curve for the dissimilarities between sites not in
the same group.}
+ \item{lty}{vector of at most length 2 (elements past the second in
+ longer vectors are ignored) line types. The first element of
+ \code{lty} will be used where a single line is drawn on a
+ plot. Where two lines are drawn (for analogue and non-analogue
+ cases), the first element pertains to the analogue group and the
+ second element to the non-analogue group. See \code{\link{par}} for
+ the allowed line types.}
\item{caption}{vector of character strings, containing the captions to
appear above each plot.}
\item{legend}{character; position of legends drawn on plots. See
@@ -130,7 +138,6 @@
One or more plots, drawn on the current device.
}
\references{
-
Brown, C.D., and Davis, H.T. (2006) Receiver operating characteristics
curves and related decision measures: A tutorial. \emph{Chemometrics
and Intelligent Laboratory Systems} \bold{80}, 24--38.
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