[Robast-commits] r723 - in branches/robast-1.0/pkg/RobAStBase: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 24 21:55:47 CET 2014
Author: ruckdeschel
Date: 2014-02-24 21:55:46 +0100 (Mon, 24 Feb 2014)
New Revision: 723
Modified:
branches/robast-1.0/pkg/RobAStBase/R/comparePlot.R
branches/robast-1.0/pkg/RobAStBase/R/ddPlot.R
branches/robast-1.0/pkg/RobAStBase/R/ddPlot_utils.R
branches/robast-1.0/pkg/RobAStBase/R/infoPlot.R
branches/robast-1.0/pkg/RobAStBase/R/outlyingPlot.R
branches/robast-1.0/pkg/RobAStBase/R/plotRescaledAxis.R
branches/robast-1.0/pkg/RobAStBase/man/ddPlot-methods.Rd
branches/robast-1.0/pkg/RobAStBase/man/internals_ddPlot.Rd
branches/robast-1.0/pkg/RobAStBase/man/outlyingPlotIC.Rd
Log:
RobAStBase: fixed some diagnostic plots:
+ comparePlot now plots the whole range
+ ddPlots / outlyingPlot.R now have alpha transparency and jitter and cex.pts
+ infoPlot plots the correct y-axis (no overplotting)
Modified: branches/robast-1.0/pkg/RobAStBase/R/comparePlot.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/comparePlot.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/comparePlot.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -28,7 +28,8 @@
expand.dots = FALSE)$"..."
dotsP <- dots
dotsLeg <- dotsT <- dotsL <- .makedotsLowLevel(dots)
-
+ dots.points <- .makedotsPt(dots)
+
ncomp <- 2+ (!missing(obj3)|!is.null(obj3)) +
(!missing(obj4)|!is.null(obj4))
@@ -321,13 +322,21 @@
matp <- cbind(matp,resc4$Y)
}
- do.call(plot, args=c(list(x = resc1$X, y = matp[,1],
- type = plty, lty = lty, col = col[1], lwd = lwd,
- xlab = xlab, ylab = ylab), dotsP, list(panel.last = pL)))
-
- do.call(matlines, args = c(list( x = resc1$X, y = matp[,-1],
- lty = lty, col = col[-1], lwd = lwd), dotsL))
+ ym <- min(matp,na.rm=T)
+ yM <- max(matp,na.rm=T)
+ y0 <- matp[,1]
+ y0[1:2] <- c(ym,yM)
+ do.call(plot, args=c(list(x = resc1$X, y = y0,
+ type = "n", xlab = xlab, ylab = ylab,
+ lty = lty[1], col = addAlphTrsp2col(col[1],0),
+ lwd = lwd[1]), dotsP, list(panel.last = pL)))
+ if(plty=="p")
+ do.call(matpoints, args = c(list( x = resc1$X, y = matp,
+ col = col), dots.points))
+ do.call(matlines, args = c(list( x = resc1$X, y = matp,
+ lty = lty, col = col, lwd = lwd), dotsL))
+
.plotRescaledAxis(scaleX, scaleX.fct, scaleX.inv,
scaleY,scaleY.fct, scaleY.inv, xlim[,i],
ylim[,i], resc1$X, ypts = 400, n = scaleN,
Modified: branches/robast-1.0/pkg/RobAStBase/R/ddPlot.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/ddPlot.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/ddPlot.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -3,7 +3,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -24,7 +24,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -45,7 +45,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff,
text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
Modified: branches/robast-1.0/pkg/RobAStBase/R/ddPlot_utils.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/ddPlot_utils.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/ddPlot_utils.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -8,7 +8,10 @@
transform.x,
transform.y = transform.x,
id.n,
+ cex.pts = 1,
lab.pts,
+ jitt.pts = 0,
+ alpha.trsp = NA,
adj =0,
cex.idn = 1,
col.idn = par("col"),
@@ -29,6 +32,12 @@
dots <- match.call(expand.dots = FALSE)$"..."
+ jitt.pts <- rep(jitt.pts,length.out=2)
+
+ col <- if(is.null(dots$col)) par("col") else dots$col
+ if(!is.na(alpha.trsp)) col <- addAlphTrsp2col(col, alpha.trsp)
+
+
id.n1 <- 1:ncol(data)
if(missing(id.n) || is.null(id.n))
@@ -116,6 +125,8 @@
if(missing(font.abline) && !is.null(dots$font)) font.abline <- dots$font
pdots <- .makedotsLowLevel(dots)
+ pdots$pch <- if(is.null(dots$pch)) "." else dots$pch
+ pdots$cex <- cex.pts
pdots$xlab <- dots$xlab
pdots$ylab <- dots$ylab
pdots$nsim <- NULL
@@ -232,12 +243,16 @@
id0.x <- id.n1[id.x]
id0.y <- id.n1[id.y]
- if(any(duplicated(ndata.x)&duplicated(ndata.y))){
- ndata.x <- jitter(ndata.x, factor=jitt.fac)
- ndata.y <- jitter(ndata.y, factor=jitt.fac)
- }
+ ndata.x0 <- ndata.x
+ ndata.y0 <- ndata.y
+ isna <- is.na(ndata.x0)|is.na(ndata.y0)
+ if(any(duplicated(ndata.x0[!isna])))
+ ndata.x0[!isna] <- jitter(ndata.x0[!isna], factor=jitt.pts[1])
+ if(any(duplicated(ndata.y0[!isna])))
+ ndata.y0[!isna] <- jitter(ndata.y0[!isna], factor=jitt.pts[2])
- do.call(plot, args = c(list(x = ndata.x, y=ndata.y, type = "p"), pdots))
+ pdots$col <- col
+ do.call(plot, args = c(list(x = ndata.x0, y=ndata.y0, type = "p"), pdots))
do.call(box,args=c(adots))
pusr <- par("usr")
Modified: branches/robast-1.0/pkg/RobAStBase/R/infoPlot.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/infoPlot.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/infoPlot.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -443,8 +443,8 @@
dotsP1))
do.call(lines, args=c(list(resc$X, resc$Y, type = plty,
lty = lty, lwd = lwd, col = col), dotsL))
- scaleX0 <- (xaxt0[1]!="n")
- scaleY0 <- (yaxt0[1]!="n")
+ scaleX0 <- scaleX & (xaxt0[1]!="n")
+ scaleY0 <- scaleY & (yaxt0[1]!="n")
x.ticks0 <- if(xaxt0[1]!="n") x.ticks else NULL
y.ticks0 <- if(yaxt0[1]!="n") y.ticks[[1]] else NULL
.plotRescaledAxis(scaleX0, scaleX.fct, scaleX.inv,
@@ -497,8 +497,8 @@
do.call(lines, args = c(list(resc.C$X, y.vec1C, type = plty,
lty = ltyI, col = colI, lwd = lwdI), dotsL))
- scaleX0 <- (xaxt0[i+in1to.draw]!="n")
- scaleY0 <- (yaxt0[i+in1to.draw]!="n")
+ scaleX0 <- scaleX & (xaxt0[i+in1to.draw]!="n")
+ scaleY0 <- scaleY & (yaxt0[i+in1to.draw]!="n")
x.ticks0 <- if(xaxt0[i+in1to.draw]!="n") x.ticks else NULL
y.ticks0 <- if(yaxt0[i+in1to.draw]!="n") y.ticks[[i+in1to.draw]] else NULL
.plotRescaledAxis(scaleX0, scaleX.fct, scaleX.inv,
Modified: branches/robast-1.0/pkg/RobAStBase/R/outlyingPlot.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/outlyingPlot.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/outlyingPlot.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -9,8 +9,11 @@
cutoff.quantile.x = 0.95,
cutoff.quantile.y = cutoff.quantile.x,
id.n,
- lab.pts,
- adj,
+ cex.pts = 1,
+ lab.pts,
+ jitt.pts = 0,
+ alpha.trsp = NA,
+ adj,
cex.idn,
col.idn,
lty.cutoff,
@@ -25,6 +28,7 @@
){
mc <- as.list(match.call(expand.dots = FALSE))[-1]
dots <- mc$"..."
+
if(is.null(dots$xlim)) dots$xlim <- TRUE
if(is.null(dots$ylim)) dots$ylim <- TRUE
if(is.null(mc$cutoff.quantile.x)) mc$cutoff.quantile.x <- 0.95
@@ -130,6 +134,8 @@
transform.y = tf.y,
id.n = mc$id.n,
lab.pts = mc$lab.pts,
+ alpha.trsp = alpha.trsp,
+ cex.pts = cex.pts,
adj = mc$adj,
cex.idn = mc$cex.idn,
col.idn = mc$col.idn,
Modified: branches/robast-1.0/pkg/RobAStBase/R/plotRescaledAxis.R
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/R/plotRescaledAxis.R 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/R/plotRescaledAxis.R 2014-02-24 20:55:46 UTC (rev 723)
@@ -100,7 +100,7 @@
if(-Inf %in% x.ticks) axis(1,at=0,labels=expression(-infinity))
if(Inf %in% x.ticks) axis(1,at=1,labels=expression(infinity))
}
- box()
+ if(withbox) box()
}else{
if(!is.null(x.ticks)){
if(is.null(xlim)){ xlim <- c(-Inf,Inf)}else{
@@ -111,7 +111,7 @@
axis(1,at=xf,labels=xf)
if(-Inf %in% x.ticks) axis(1,at=0,labels=expression(-infinity))
if(Inf %in% x.ticks) axis(1,at=1,labels=expression(infinity))
- box()
+ if(withbox) box()
}
}
if(scaleY){
@@ -150,7 +150,7 @@
if(-Inf %in% y.ticks) axis(2,at=0,labels=expression(-infinity))
if(Inf %in% y.ticks) axis(2,at=1,labels=expression(infinity))
}
- box()
+ if(withbox) box()
}else{
if(!is.null(y.ticks)){
if(is.null(ylim)){ ylim <- c(-Inf,Inf)}else{
@@ -161,7 +161,7 @@
axis(2,at=yf,labels=yf)
if(-Inf %in% y.ticks) axis(2,at=0,labels=expression(-infinity))
if(Inf %in% y.ticks) axis(2,at=1,labels=expression(infinity))
- box()
+ if(withbox) box()
}
}
return(invisible(NULL))
Modified: branches/robast-1.0/pkg/RobAStBase/man/ddPlot-methods.Rd
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/man/ddPlot-methods.Rd 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/man/ddPlot-methods.Rd 2014-02-24 20:55:46 UTC (rev 723)
@@ -13,7 +13,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -27,7 +27,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -41,7 +41,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -69,7 +69,18 @@
distances of the \code{y} axis.}
\item{id.n}{a set of indices (or a corresponding logical vector); to select a subset
of the data in argument \code{data}.}
+ \item{cex.pts}{the corresponding \code{cex} argument for plotted points.}
\item{lab.pts}{a vector of labels for the (unsubsetted) \code{data}.}
+ \item{jitt.pts}{the corresponding \code{jitter} argument for plotted points;
+ may be a vector of length 2 -- for separate factors for x- and y-coordinate.}
+ \item{alpha.trsp}{alpha transparency to be added ex post to colors
+ \code{col.pch} and \code{col.lbl}; if one-dim and NA all colors are
+ left unchanged. Otherwise, with usual recycling rules \code{alpha.trsp}
+ gets shorted/prolongated to length the data-symbols to be plotted.
+ Coordinates of this vector \code{alpha.trsp} with NA are left unchanged,
+ while for the remaining ones, the alpha channel in rgb space is set
+ to the respective coordinate value of \code{alpha.trsp}. The non-NA
+ entries must be integers in [0,255] (0 invisible, 255 opaque).}
\item{adj}{the corresponding argument for \code{\link[graphics]{text}} for
labelling the outliers.}
\item{cex.idn}{the corresponding \code{cex} argument for
Modified: branches/robast-1.0/pkg/RobAStBase/man/internals_ddPlot.Rd
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/man/internals_ddPlot.Rd 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/man/internals_ddPlot.Rd 2014-02-24 20:55:46 UTC (rev 723)
@@ -13,7 +13,7 @@
cutoff.y = cutoff(norm = dist.y, cutoff.quantile = cutoff.quantile.y),
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj =0, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff,
lwd.cutoff, col.cutoff = "red", text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
@@ -43,7 +43,18 @@
distances of the \code{y} axis.}
\item{id.n}{a set of indices (or a corresponding logical vector); to select a subset
of the data in argument \code{data}.}
+ \item{cex.pts}{the corresponding \code{cex} argument for plotted points.}
\item{lab.pts}{a vector of labels for the (unsubsetted) \code{data}.}
+ \item{jitt.pts}{the corresponding \code{jitter} argument for plotted points;
+ may be a vector of length 2 -- for separate factors for x- and y-coordinate.}
+ \item{alpha.trsp}{alpha transparency to be added ex post to colors
+ \code{col.pch} and \code{col.lbl}; if one-dim and NA all colors are
+ left unchanged. Otherwise, with usual recycling rules \code{alpha.trsp}
+ gets shorted/prolongated to length the data-symbols to be plotted.
+ Coordinates of this vector \code{alpha.trsp} with NA are left unchanged,
+ while for the remaining ones, the alpha channel in rgb space is set
+ to the respective coordinate value of \code{alpha.trsp}. The non-NA
+ entries must be integers in [0,255] (0 invisible, 255 opaque).}
\item{adj}{the corresponding argument for \code{\link[graphics]{text}} for
labelling the outliers.}
\item{cex.idn}{the corresponding \code{cex} argument for
Modified: branches/robast-1.0/pkg/RobAStBase/man/outlyingPlotIC.Rd
===================================================================
--- branches/robast-1.0/pkg/RobAStBase/man/outlyingPlotIC.Rd 2014-02-24 17:58:37 UTC (rev 722)
+++ branches/robast-1.0/pkg/RobAStBase/man/outlyingPlotIC.Rd 2014-02-24 20:55:46 UTC (rev 723)
@@ -7,8 +7,9 @@
outlyingPlotIC(data, IC.x, IC.y = IC.x, dist.x = NormType(),
dist.y, cutoff.y = cutoff.chisq(), cutoff.x = cutoff.sememp(),
..., cutoff.quantile.x = 0.95,
- cutoff.quantile.y = cutoff.quantile.x, id.n, lab.pts, adj,
- cex.idn, col.idn, lty.cutoff, lwd.cutoff, col.cutoff,
+ cutoff.quantile.y = cutoff.quantile.x,
+ id.n, cex.pts = 1,lab.pts, jitt.pts = 0, alpha.trsp = NA,
+ adj =0, cex.idn, col.idn, lty.cutoff, lwd.cutoff, col.cutoff,
robCov.x = TRUE, robCov.y = TRUE, tf.x = data, tf.y = data,
jitt.fac = 10,
main = gettext("Outlyingness \n by means of a distance-distance plot")
@@ -31,7 +32,18 @@
\item{cutoff.quantile.y}{numeric; the cutoff quantile for the \code{y} axis.}
\item{id.n}{a set of indices (or a corresponding logical vector); to select a subset
of the data in argument \code{data}.}
+ \item{cex.pts}{the corresponding \code{cex} argument for plotted points.}
\item{lab.pts}{a vector of labels for the (unsubsetted) \code{data}.}
+ \item{jitt.pts}{the corresponding \code{jitter} argument for plotted points;
+ may be a vector of length 2 -- for separate factors for x- and y-coordinate.}
+ \item{alpha.trsp}{alpha transparency to be added ex post to colors
+ \code{col.pch} and \code{col.lbl}; if one-dim and NA all colors are
+ left unchanged. Otherwise, with usual recycling rules \code{alpha.trsp}
+ gets shorted/prolongated to length the data-symbols to be plotted.
+ Coordinates of this vector \code{alpha.trsp} with NA are left unchanged,
+ while for the remaining ones, the alpha channel in rgb space is set
+ to the respective coordinate value of \code{alpha.trsp}. The non-NA
+ entries must be integers in [0,255] (0 invisible, 255 opaque).}
\item{adj}{the corresponding argument for \code{\link[graphics]{text}} for
labelling the outliers.}
\item{cex.idn}{the corresponding \code{cex} argument for
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