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# pROC: Tools Receiver operating characteristic (ROC curves) with
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# (partial) area under the curve, confidence intervals and comparison.
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# Copyright (C) 2010-2014 Xavier Robin, Alexandre Hainard, Natacha Turck,
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# Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez
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# and Markus Müller
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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plot.ci.thresholds <- function(x, length=.01*ifelse(attr(x, "roc")$percent, 100, 1), col=par("fg"), ...) {
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bounds <- cbind(x$sp, x$se)
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apply(bounds, 1, function(x, ...) {
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suppressWarnings(segments(x[2], x[4], x[2], x[6], col=col, ...))
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suppressWarnings(segments(x[2] - length, x[4], x[2] + length, x[4], col=col, ...))
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suppressWarnings(segments(x[2] - length, x[6], x[2] + length, x[6], col=col, ...))
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suppressWarnings(segments(x[1], x[5], x[3], x[5], col=col, ...))
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suppressWarnings(segments(x[1], x[5] + length, x[1], x[5] - length, col=col, ...))
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suppressWarnings(segments(x[3], x[5] + length, x[3], x[5] - length, col=col, ...))
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}, ...)
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invisible(x)
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}
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plot.ci.sp <- function(x, type=c("bars", "shape"), length=.01*ifelse(attr(x, "roc")$percent, 100, 1), col=ifelse(type=="bars", par("fg"), "gainsboro"), no.roc=FALSE, ...) {
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type <- match.arg(type)
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if (type == "bars") {
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sapply(1:dim(x)[1], function(n, ...) {
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se <- attr(x, "sensitivities")[n]
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suppressWarnings(segments(x[n,1], se, x[n,3], se, col=col, ...))
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suppressWarnings(segments(x[n,1], se - length, x[n,1], se + length, col=col, ...))
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suppressWarnings(segments(x[n,3], se - length, x[n,3], se + length, col=col, ...))
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}, ...)
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}
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else {
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if (length(x[,1]) < 15)
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warning("Low definition shape.")
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suppressWarnings(polygon(c(1*ifelse(attr(x, "roc")$percent, 100, 1), x[,1], 0, rev(x[,3]), 1*ifelse(attr(x, "roc")$percent, 100, 1)), c(0, attr(x, "sensitivities"), 1*ifelse(attr(x, "roc")$percent, 100, 1), rev(attr(x, "sensitivities")), 0), col=col, ...))
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if (!no.roc)
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plot(attr(x, "roc"), add=TRUE)
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}
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invisible(x)
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}
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plot.ci.se <- function(x, type=c("bars", "shape"), length=.01*ifelse(attr(x, "roc")$percent, 100, 1), col=ifelse(type=="bars", par("fg"), "gainsboro"), no.roc=FALSE, ...) {
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type <- match.arg(type)
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if (type == "bars") {
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sapply(1:dim(x)[1], function(n, ...) {
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sp <- attr(x, "specificities")[n]
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suppressWarnings(segments(sp, x[n,1], sp, x[n,3], col=col, ...))
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suppressWarnings(segments(sp - length, x[n,1], sp + length, x[n,1], col=col, ...))
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suppressWarnings(segments(sp - length, x[n,3], sp + length, x[n,3], col=col, ...))
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}, ...)
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}
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else {
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if (length(x[,1]) < 15)
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warning("Low definition shape.")
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suppressWarnings(polygon(c(0, attr(x, "specificities"), 1*ifelse(attr(x, "roc")$percent, 100, 1), rev(attr(x, "specificities")), 0), c(1*ifelse(attr(x, "roc")$percent, 100, 1), x[,1], 0, rev(x[,3]), 1*ifelse(attr(x, "roc")$percent, 100, 1)), col=col, ...))
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if (!no.roc)
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plot(attr(x, "roc"), add=TRUE)
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}
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invisible(x)
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}
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xrobin