R/stats_plot3d.R
In simscr/metaboanalyst: An R Package for Comprehensive Analysis of Metabolomics Data
Defines functions
Plot3D
PlotPCA3DScoreImg
PlotSPLS3DScoreImg
PlotSPLS3DScoreImg
PlotPLS3DScoreImg
Documented in
PlotPCA3DScoreImg
PlotPLS3DScoreImg
PlotSPLS3DScoreImg
### R script for MetaboAnalyst
### Description: 3D scatter plot for PDF report (not used for web display)
### Author: Jeff Xia, jeff.xia@mcgill.ca
### McGill University, Canada
### License: GNU GPL (>= 2)
Plot3D <- function(x, y = NULL, z = NULL, color = par("col"), pch = NULL,
main = NULL, sub = NULL, xlim = NULL, ylim = NULL, zlim = NULL,
xlab = NULL, ylab = NULL, zlab = NULL, scale.y = 1, angle = 40,
axis = TRUE, tick.marks = TRUE, label.tick.marks = TRUE,
x.ticklabs = NULL, y.ticklabs = NULL, z.ticklabs = NULL,
y.margin.add = 0, grid = TRUE, box = TRUE, lab = par("lab"),
lab.z = mean(lab[1:2]), type = "p", highlight.3d = FALSE,
mar = c(5, 3, 4, 3) + 0.1, col.axis = par("col.axis"),
col.grid = "grey", col.lab = par("col.lab"), cex.symbols = par("cex"),
cex.axis = 0.8 * par("cex.axis"), cex.lab = par("cex.lab"),
font.axis = par("font.axis"), font.lab = par("font.lab"),
lty.axis = par("lty"), lty.grid = 2, lty.hide = 1,
lty.hplot = par("lty"), log = "", ...)
# log not yet implemented
{
## Uwe Ligges <ligges@statistik.tu-dortmund.de>,
## http://www.statistik.tu-dortmund.de/~ligges
##
## For MANY ideas and improvements thanks to Martin Maechler!!!
## Parts of the help files are stolen from the standard plotting functions in R.
mem.par <- par(mar = mar)
x.scal <- y.scal <- z.scal <- 1
xlabel <- if (!missing(x)) deparse(substitute(x))
ylabel <- if (!missing(y)) deparse(substitute(y))
zlabel <- if (!missing(z)) deparse(substitute(z))
## color as part of `x' (data.frame or list):
if(!is.null(d <- dim(x)) && (length(d) == 2) && (d[2] >= 4))
color <- x[,4]
else if(is.list(x) && !is.null(x$color))
color <- x$color
## convert 'anything' -> vector
xyz <- xyz.coords(x=x, y=y, z=z, xlab=xlabel, ylab=ylabel, zlab=zlabel,
log=log)
if(is.null(xlab)) { xlab <- xyz$xlab; if(is.null(xlab)) xlab <- "" }
if(is.null(ylab)) { ylab <- xyz$ylab; if(is.null(ylab)) ylab <- "" }
if(is.null(zlab)) { zlab <- xyz$zlab; if(is.null(zlab)) zlab <- "" }
if(length(color) == 1)
color <- rep(color, length(xyz$x))
else if(length(color) != length(xyz$x))
stop("length(color) ", "must be equal length(x) or 1")
angle <- (angle %% 360) / 90
yz.f <- scale.y * abs(if(angle < 1) angle else if(angle > 3) angle - 4 else 2 - angle)
yx.f <- scale.y * (if(angle < 2) 1 - angle else angle - 3)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
temp <- xlab; xlab <- ylab; ylab <- temp
temp <- xlim; xlim <- ylim; ylim <- temp
}
angle.1 <- (1 < angle && angle < 2) || angle > 3
angle.2 <- 1 <= angle && angle <= 3
dat <- cbind(as.data.frame(xyz[c("x","y","z")]), col = color)
n <- nrow(dat);
y.range <- range(dat$y[is.finite(dat$y)])
### 3D-highlighting / colors / sort by y
if(type == "p" || type == "h") {
y.ord <- rev(order(dat$y))
dat <- dat[y.ord, ]
if(length(pch) > 1)
if(length(pch) != length(y.ord))
stop("length(pch) ", "must be equal length(x) or 1")
else pch <- pch[y.ord]
daty <- dat$y
daty[!is.finite(daty)] <- mean(daty[is.finite(daty)])
if(highlight.3d && !(all(diff(daty) == 0)))
dat$col <- rgb(seq(0, 1, length = n) * (y.range[2] - daty) / diff(y.range), g=0, b=0)
}
### optim. axis scaling
p.lab <- par("lab")
## Y
y.range <- range(dat$y[is.finite(dat$y)], ylim)
y.prty <- pretty(y.range, n = lab[2],
min.n = max(1, min(.5 * lab[2], p.lab[2])))
y.scal <- round(diff(y.prty[1:2]), digits = 12)
y.add <- min(y.prty)
dat$y <- (dat$y - y.add) / y.scal
y.max <- (max(y.prty) - y.add) / y.scal
x.range <- range(dat$x[is.finite(dat$x)], xlim)
x.prty <- pretty(x.range, n = lab[1],
min.n = max(1, min(.5 * lab[1], p.lab[1])))
x.scal <- round(diff(x.prty[1:2]), digits = 12)
dat$x <- dat$x / x.scal
x.range <- range(x.prty) / x.scal
x.max <- ceiling(x.range[2])
x.min <- floor(x.range[1])
if(!is.null(xlim)) {
x.max <- max(x.max, ceiling(xlim[2] / x.scal))
x.min <- min(x.min, floor(xlim[1] / x.scal))
}
x.range <- range(x.min, x.max)
## Z
z.range <- range(dat$z[is.finite(dat$z)], zlim)
z.prty <- pretty(z.range, n = lab.z,
min.n = max(1, min(.5 * lab.z, p.lab[2])))
z.scal <- round(diff(z.prty[1:2]), digits = 12)
dat$z <- dat$z / z.scal
z.range <- range(z.prty) / z.scal
z.max <- ceiling(z.range[2])
z.min <- floor(z.range[1])
if(!is.null(zlim)) {
z.max <- max(z.max, ceiling(zlim[2] / z.scal))
z.min <- min(z.min, floor(zlim[1] / z.scal))
}
z.range <- range(z.min, z.max)
### init graphics
plot.new()
if(angle.2) {x1 <- x.min + yx.f * y.max; x2 <- x.max}
else {x1 <- x.min; x2 <- x.max + yx.f * y.max}
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
temp <- strwidth(format(rev(y.prty))[1], cex = cex.axis/par("cex"))
if(angle.2) x1 <- x1 - temp - y.margin.add
else x2 <- x2 + temp + y.margin.add
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
if(angle > 2) par("usr" = par("usr")[c(2, 1, 3:4)])
usr <- par("usr") # we have to remind it for use in closures
title(main, sub, ...)
### draw axis, tick marks, labels, grid, ...
xx <- if(angle.2) c(x.min, x.max) else c(x.max, x.min)
if(grid) {
## grids
###################
# XY wall
i <- x.min:x.max;
segments(i, z.min, i + (yx.f * y.max), yz.f * y.max + z.min,
col = col.grid, lty = lty.grid);
i <- 0:y.max;
segments(x.min + (i * yx.f), i * yz.f + z.min,
x.max + (i * yx.f), i * yz.f + z.min,
col = col.grid, lty = lty.grid);
######################
# XZ wall
# verticle lines
temp <- yx.f * y.max;
temp1 <- yz.f * y.max;
i <- (x.min + temp):(x.max + temp);
segments(i, z.min + temp1, i, z.max + temp1,
col = col.grid, lty = lty.grid);
# horizontal lines
i <- (z.min + temp1):(z.max + temp1);
segments(x.min + temp, i, x.max + temp, i,
col = col.grid, lty = lty.grid)
##################
# YZ wall
# horizontal lines
i <- xx[2]:x.min;
mm <- z.min:z.max;
segments(i, mm, i + temp, mm + temp1,
col = col.grid, lty = lty.grid);
# verticle lines
i <- 0:y.max;
segments(x.min + (i * yx.f), i * yz.f + z.min,
xx[2] + (i * yx.f), i * yz.f + z.max,
col = col.grid, lty = lty.grid)
# make the axis into solid line
segments(x.min, z.min, x.min + (yx.f * y.max), yz.f * y.max + z.min,
col = col.grid, lty = lty.hide);
segments(x.max, z.min, x.max + (yx.f * y.max), yz.f * y.max + z.min,
col = col.axis, lty = lty.hide);
segments(x.min + (y.max * yx.f), y.max * yz.f + z.min,
x.max + (y.max* yx.f), y.max * yz.f + z.min,
col = col.grid, lty = lty.hide);
segments(x.min + temp, z.min + temp1, x.min + temp, z.max + temp1,
col = col.grid, lty = lty.hide);
segments(x.max + temp, z.min + temp1, x.max + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
segments(x.min + temp, z.max + temp1, x.max + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
segments(xx[2], z.max, xx[2] + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
}
if(axis) {
if(tick.marks) { ## tick marks
xtl <- (z.max - z.min) * (tcl <- -par("tcl")) / 50
ztl <- (x.max - x.min) * tcl / 50
mysegs <- function(x0,y0, x1,y1)
segments(x0,y0, x1,y1, col=col.axis, lty=lty.axis)
## Y
i.y <- 0:y.max
mysegs(yx.f * i.y - ztl + xx[1], yz.f * i.y + z.min,
yx.f * i.y + ztl + xx[1], yz.f * i.y + z.min)
## X
i.x <- x.min:x.max
mysegs(i.x, -xtl + z.min, i.x, xtl + z.min)
## Z
i.z <- z.min:z.max
mysegs(-ztl + xx[2], i.z, ztl + xx[2], i.z)
if(label.tick.marks) { ## label tick marks
las <- par("las")
mytext <- function(labels, side, at, ...)
mtext(text = labels, side = side, at = at, line = -.5,
col=col.lab, cex=cex.axis, font=font.lab, ...)
## X
if(is.null(x.ticklabs))
x.ticklabs <- format(i.x * x.scal)
mytext(x.ticklabs, side = 1, at = i.x)
## Z
if(is.null(z.ticklabs))
z.ticklabs <- format(i.z * z.scal)
mytext(z.ticklabs, side = if(angle.1) 4 else 2, at = i.z,
adj = if(0 < las && las < 3) 1 else NA)
## Y
temp <- if(angle > 2) rev(i.y) else i.y ## turn y-labels around
if(is.null(y.ticklabs))
y.ticklabs <- format(y.prty)
else if (angle > 2)
y.ticklabs <- rev(y.ticklabs)
text(i.y * yx.f + xx[1],
i.y * yz.f + z.min, y.ticklabs,
pos=if(angle.1) 2 else 4, offset=1,
col=col.lab, cex=cex.axis/par("cex"), font=font.lab)
}
}
## axis and labels
mytext2 <- function(lab, side, line, at)
mtext(lab, side = side, line = line, at = at, col = col.lab,
cex = cex.lab, font = font.axis, las = 0)
## X
lines(c(x.min, x.max), c(z.min, z.min), col = col.axis, lty = lty.axis)
mytext2(xlab, 1, line = 1.5, at = mean(x.range))
## Y
lines(xx[1] + c(0, y.max * yx.f), c(z.min, y.max * yz.f + z.min),
col = col.axis, lty = lty.axis)
mytext2(ylab, if(angle.1) 2 else 4, line= 0.5, at = z.min + y.max * yz.f)
## Z
lines(xx[c(2,2)], c(z.min, z.max), col = col.axis, lty = lty.axis)
mytext2(zlab, if(angle.1) 4 else 2, line= 1.5, at = mean(z.range))
}
### plot points
x <- dat$x + (dat$y * yx.f)
z <- dat$z + (dat$y * yz.f)
col <- as.character(dat$col)
if(type == "h") {
z2 <- dat$y * yz.f + z.min
segments(x, z, x, z2, col = col, cex = cex.symbols, lty = lty.hplot, ...)
points(x, z, type = "p", col = col, pch = pch, cex = cex.symbols, ...)
}
else points(x, z, type = type, col = col, pch = pch, cex = cex.symbols, ...)
### box-lines in front of points (overlay)
if(axis && box) {
lines(c(x.min, x.max), c(z.max, z.max),
col = col.axis, lty = lty.axis)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max,
col = col.axis, lty = lty.axis)
lines(xx[c(1,1)], c(z.min, z.max), col = col.axis, lty = lty.axis)
}
# par(mem.par) # we MUST NOT set the margins back
### Return Function Object
ob <- ls() ## remove all unused objects from the result's enviroment:
rm(list = ob[!ob %in% c("angle", "mar", "usr", "x.scal", "y.scal", "z.scal", "yx.f",
"yz.f", "y.add", "z.min", "z.max", "x.min", "x.max", "y.max",
"x.prty", "y.prty", "z.prty")])
rm(ob)
invisible(list(
xyz.convert = function(x, y=NULL, z=NULL) {
xyz <- xyz.coords(x, y, z)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
}
y <- (xyz$y - y.add) / y.scal
return(list(x = xyz$x / x.scal + yx.f * y,
y = xyz$z / z.scal + yz.f * y))
},
points3d = function(x, y = NULL, z = NULL, type = "p", ...) {
xyz <- xyz.coords(x, y, z)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
}
y2 <- (xyz$y - y.add) / y.scal
x <- xyz$x / x.scal + yx.f * y2
y <- xyz$z / z.scal + yz.f * y2
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
if(type == "h") {
y2 <- z.min + yz.f * y2
segments(x, y, x, y2, ...)
points(x, y, type = "p", ...)
}
else points(x, y, type = type, ...)
},
plane3d = function(Intercept, x.coef = NULL, y.coef = NULL,
lty = "dashed", lty.box = NULL, ...){
if(!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept)
if(is.null(lty.box)) lty.box <- lty
if(is.null(x.coef) && length(Intercept) == 3){
x.coef <- Intercept[if(angle > 2) 3 else 2]
y.coef <- Intercept[if(angle > 2) 2 else 3]
Intercept <- Intercept[1]
}
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
x <- x.min:x.max
ltya <- c(lty.box, rep(lty, length(x)-2), lty.box)
x.coef <- x.coef * x.scal
z1 <- (Intercept + x * x.coef + y.add * y.coef) / z.scal
z2 <- (Intercept + x * x.coef +
(y.max * y.scal + y.add) * y.coef) / z.scal
segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max, lty = ltya, ...)
y <- 0:y.max
ltya <- c(lty.box, rep(lty, length(y)-2), lty.box)
y.coef <- (y * y.scal + y.add) * y.coef
z1 <- (Intercept + x.min * x.coef + y.coef) / z.scal
z2 <- (Intercept + x.max * x.coef + y.coef) / z.scal
segments(x.min + y * yx.f, z1 + y * yz.f,
x.max + y * yx.f, z2 + y * yz.f, lty = ltya, ...)
},
wall3d = function(Intercept, x.coef = NULL, y.coef = NULL,
lty = "dashed", lty.box = NULL, ...){
if(!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept)
if(is.null(lty.box)) lty.box <- lty
if(is.null(x.coef) && length(Intercept) == 3){
x.coef <- Intercept[if(angle > 2) 3 else 2]
y.coef <- Intercept[if(angle > 2) 2 else 3]
Intercept <- Intercept[1]
}
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
x <- x.min:x.max
ltya <- c(lty.box, rep(lty, length(x)-2), lty.box)
x.coef <- x.coef * x.scal
z1 <- (Intercept + x * x.coef + y.add * y.coef) / z.scal
z2 <- (Intercept + x * x.coef +
(y.max * y.scal + y.add) * y.coef) / z.scal
segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max, lty = ltya, ...)
y <- 0:y.max
ltya <- c(lty.box, rep(lty, length(y)-2), lty.box)
y.coef <- (y * y.scal + y.add) * y.coef
z1 <- (Intercept + x.min * x.coef + y.coef) / z.scal
z2 <- (Intercept + x.max * x.coef + y.coef) / z.scal
segments(x.min + y * yx.f, z1 + y * yz.f,
x.max + y * yx.f, z2 + y * yz.f, lty = ltya, ...)
},
box3d = function(...){
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
lines(c(x.min, x.max), c(z.max, z.max), ...)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max, ...)
lines(c(0, y.max * yx.f) + x.min, c(0, y.max * yz.f) + z.max, ...)
lines(c(x.max, x.max), c(z.min, z.max), ...)
lines(c(x.min, x.min), c(z.min, z.max), ...)
lines(c(x.min, x.max), c(z.min, z.min), ...)
}
))
}
#'Create 3D PCA score plot
#'@description This function creates both a static 3D PCA score plot as well as an interactive 3D PCA score plot
#'using the plotly R package. The 3D PCA score plot is stored in the mSetObj (mSetObj$imgSet$pca.3d). To view
#'the plot, if your mSetObj is named mSet, type "mSet$imgSet$pca.3d" inro your R console, and the 3D plot will appear.
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@usage PlotPCA3DScoreImg(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl)
#'@param mSetObj Input name of the created mSet Object.
#'@param imgName Input a name for the plot.
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@usage mSet <- PlotPCA3DScore(mSetObj=NA, imgName, format="json", dpi=72, width=NA, inx1, inx2, inx3, angl)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotPCA3DScoreImg <- function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
xlabel = paste("PC",inx1, "(", round(100*mSetObj$analSet$pca$variance[inx1],1), "%)");
ylabel = paste("PC",inx2, "(", round(100*mSetObj$analSet$pca$variance[inx2],1), "%)");
zlabel = paste("PC",inx3, "(", round(100*mSetObj$analSet$pca$variance[inx3],1), "%)");
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$pca.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
if(mSetObj$dataSet$cls.type == "disc"){
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
Plot3D(mSetObj$analSet$pca$x[, inx1], mSetObj$analSet$pca$x[, inx2], mSetObj$analSet$pca$x[, inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, color=cols, pch=pchs, box=F);
legend("topleft", legend =legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = mSetObj$analSet$pca$x[, inx1], y = mSetObj$analSet$pca$x[, inx2], z = mSetObj$analSet$pca$x[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$pca.3d <- p;
print("The Interactive 3D PCA plot has been created, please find it in mSet$imgSet$pca.3d.")
}
}else{
Plot3D(mSetObj$analSet$pca$x[, inx1], mSetObj$analSet$pca$x[, inx2], mSetObj$analSet$pca$x[, inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, pch=pchs, box=F);
dev.off();
if(!.on.public.web){
# 3D View using plotly
col <- c("#C61951", "#1972A4")
p <- plotly::plot_ly(x = mSetObj$analSet$pca$x[, inx1], y = mSetObj$analSet$pca$x[, inx2], z = mSetObj$analSet$pca$x[, inx3],
color = pchs, colors = col, marker = list(colorbar = list(len = 1, tickmode = array, tickvals = range(unique(pchs)),
ticktext = levels(mSetObj$dataSet$cls))));
p <- plotly::add_markers(p, sizes = 1000);
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)));
mSetObj$imgSet$pca.3d <- p;
print("The Interactive 3D PCA plot has been created, please find it in mSet$imgSet$pca.3d.")
}
}
return(.set.mSet(mSetObj));
}
#'Plot sPLS-DA 3D score plot
#'@description This function creates two 3D sPLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$splsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$splsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotSPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$spls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
spls3d <- list();
## need to check if only 2 or 3 components generated
if(length(mSetObj$analSet$splsr$explained_variance$X)==2){
spls3d$score$axis <- paste("Component", c(inx1, inx2), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2)], 5));
spls3d$score$axis <- c(spls3d$score$axis, "Component3 (NA)");
coords <- rbind(coords, "comp 3"=rep (0, ncol(coords)));
}else{
spls3d$score$axis <- paste("Component", c(inx1, inx2, inx3), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2, inx3)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2, inx3)], 5));
}
xlabel <- spls3d$score$axis[1]
ylabel <- spls3d$score$axis[2]
zlabel <- spls3d$score$axis[3]
# static
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(coords[,inx1], coords[,inx2], coords[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle = angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = coords[, inx1], y = coords[, inx2], z = coords[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$splsda.3d <- p;
print("The Interactive 3D sPLS-DA plot has been created, please find it in mSet$imgSet$splsda.3d.")
}
return(.set.mSet(mSetObj));
}
#'Plot sPLS-DA 3D score plot
#'@description This function creates two 3D sPLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$splsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$splsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotSPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$spls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
spls3d <- list();
## need to check if only 2 or 3 components generated
if(length(mSetObj$analSet$splsr$explained_variance$X)==2){
spls3d$score$axis <- paste("Component", c(inx1, inx2), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2)], 5));
spls3d$score$axis <- c(spls3d$score$axis, "Component3 (NA)");
coords <- rbind(coords, "comp 3"=rep (0, ncol(coords)));
}else{
spls3d$score$axis <- paste("Component", c(inx1, inx2, inx3), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2, inx3)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2, inx3)], 5));
}
xlabel <- spls3d$score$axis[1]
ylabel <- spls3d$score$axis[2]
zlabel <- spls3d$score$axis[3]
# static
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(coords[,inx1], coords[,inx2], coords[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle = angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = coords[, inx1], y = coords[, inx2], z = coords[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$splsda.3d <- p;
print("The Interactive 3D sPLS-DA plot has been created, please find it in mSet$imgSet$splsda.3d.")
}
return(.set.mSet(mSetObj));
}
#'Plot PLS 3D score plot
#'@description This function creates two 3D PLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$plsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$plsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$pls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
xlabel <- paste("Component", inx1, "(", round(100*mSetObj$analSet$plsr$Xvar[inx1]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
ylabel <- paste("Component", inx2, "(", round(100*mSetObj$analSet$plsr$Xvar[inx2]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
zlabel <- paste("Component", inx3, "(", round(100*mSetObj$analSet$plsr$Xvar[inx3]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(mSetObj$analSet$plsr$score[,inx1], mSetObj$analSet$plsr$score[,inx2], mSetObj$analSet$plsr$score[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = mSetObj$analSet$plsr$score[, inx1], y = mSetObj$analSet$plsr$score[, inx2], z = mSetObj$analSet$plsr$score[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$plsda.3d <- p;
print("The Interactive 3D PLS-DA plot has been created, please find it in mSet$imgSet$plsda.3d.")
}
return(.set.mSet(mSetObj));
}
simscr/metaboanalyst documentation built on Jan. 21, 2020, 12:13 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions Plot3D PlotPCA3DScoreImg PlotSPLS3DScoreImg PlotSPLS3DScoreImg PlotPLS3DScoreImg
Documented in PlotPCA3DScoreImg PlotPLS3DScoreImg PlotSPLS3DScoreImg
### R script for MetaboAnalyst
### Description: 3D scatter plot for PDF report (not used for web display)
### Author: Jeff Xia, jeff.xia@mcgill.ca
### McGill University, Canada
### License: GNU GPL (>= 2)
Plot3D <- function(x, y = NULL, z = NULL, color = par("col"), pch = NULL,
main = NULL, sub = NULL, xlim = NULL, ylim = NULL, zlim = NULL,
xlab = NULL, ylab = NULL, zlab = NULL, scale.y = 1, angle = 40,
axis = TRUE, tick.marks = TRUE, label.tick.marks = TRUE,
x.ticklabs = NULL, y.ticklabs = NULL, z.ticklabs = NULL,
y.margin.add = 0, grid = TRUE, box = TRUE, lab = par("lab"),
lab.z = mean(lab[1:2]), type = "p", highlight.3d = FALSE,
mar = c(5, 3, 4, 3) + 0.1, col.axis = par("col.axis"),
col.grid = "grey", col.lab = par("col.lab"), cex.symbols = par("cex"),
cex.axis = 0.8 * par("cex.axis"), cex.lab = par("cex.lab"),
font.axis = par("font.axis"), font.lab = par("font.lab"),
lty.axis = par("lty"), lty.grid = 2, lty.hide = 1,
lty.hplot = par("lty"), log = "", ...)
# log not yet implemented
{
## Uwe Ligges <ligges@statistik.tu-dortmund.de>,
## http://www.statistik.tu-dortmund.de/~ligges
##
## For MANY ideas and improvements thanks to Martin Maechler!!!
## Parts of the help files are stolen from the standard plotting functions in R.
mem.par <- par(mar = mar)
x.scal <- y.scal <- z.scal <- 1
xlabel <- if (!missing(x)) deparse(substitute(x))
ylabel <- if (!missing(y)) deparse(substitute(y))
zlabel <- if (!missing(z)) deparse(substitute(z))
## color as part of `x' (data.frame or list):
if(!is.null(d <- dim(x)) && (length(d) == 2) && (d[2] >= 4))
color <- x[,4]
else if(is.list(x) && !is.null(x$color))
color <- x$color
## convert 'anything' -> vector
xyz <- xyz.coords(x=x, y=y, z=z, xlab=xlabel, ylab=ylabel, zlab=zlabel,
log=log)
if(is.null(xlab)) { xlab <- xyz$xlab; if(is.null(xlab)) xlab <- "" }
if(is.null(ylab)) { ylab <- xyz$ylab; if(is.null(ylab)) ylab <- "" }
if(is.null(zlab)) { zlab <- xyz$zlab; if(is.null(zlab)) zlab <- "" }
if(length(color) == 1)
color <- rep(color, length(xyz$x))
else if(length(color) != length(xyz$x))
stop("length(color) ", "must be equal length(x) or 1")
angle <- (angle %% 360) / 90
yz.f <- scale.y * abs(if(angle < 1) angle else if(angle > 3) angle - 4 else 2 - angle)
yx.f <- scale.y * (if(angle < 2) 1 - angle else angle - 3)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
temp <- xlab; xlab <- ylab; ylab <- temp
temp <- xlim; xlim <- ylim; ylim <- temp
}
angle.1 <- (1 < angle && angle < 2) || angle > 3
angle.2 <- 1 <= angle && angle <= 3
dat <- cbind(as.data.frame(xyz[c("x","y","z")]), col = color)
n <- nrow(dat);
y.range <- range(dat$y[is.finite(dat$y)])
### 3D-highlighting / colors / sort by y
if(type == "p" || type == "h") {
y.ord <- rev(order(dat$y))
dat <- dat[y.ord, ]
if(length(pch) > 1)
if(length(pch) != length(y.ord))
stop("length(pch) ", "must be equal length(x) or 1")
else pch <- pch[y.ord]
daty <- dat$y
daty[!is.finite(daty)] <- mean(daty[is.finite(daty)])
if(highlight.3d && !(all(diff(daty) == 0)))
dat$col <- rgb(seq(0, 1, length = n) * (y.range[2] - daty) / diff(y.range), g=0, b=0)
}
### optim. axis scaling
p.lab <- par("lab")
## Y
y.range <- range(dat$y[is.finite(dat$y)], ylim)
y.prty <- pretty(y.range, n = lab[2],
min.n = max(1, min(.5 * lab[2], p.lab[2])))
y.scal <- round(diff(y.prty[1:2]), digits = 12)
y.add <- min(y.prty)
dat$y <- (dat$y - y.add) / y.scal
y.max <- (max(y.prty) - y.add) / y.scal
x.range <- range(dat$x[is.finite(dat$x)], xlim)
x.prty <- pretty(x.range, n = lab[1],
min.n = max(1, min(.5 * lab[1], p.lab[1])))
x.scal <- round(diff(x.prty[1:2]), digits = 12)
dat$x <- dat$x / x.scal
x.range <- range(x.prty) / x.scal
x.max <- ceiling(x.range[2])
x.min <- floor(x.range[1])
if(!is.null(xlim)) {
x.max <- max(x.max, ceiling(xlim[2] / x.scal))
x.min <- min(x.min, floor(xlim[1] / x.scal))
}
x.range <- range(x.min, x.max)
## Z
z.range <- range(dat$z[is.finite(dat$z)], zlim)
z.prty <- pretty(z.range, n = lab.z,
min.n = max(1, min(.5 * lab.z, p.lab[2])))
z.scal <- round(diff(z.prty[1:2]), digits = 12)
dat$z <- dat$z / z.scal
z.range <- range(z.prty) / z.scal
z.max <- ceiling(z.range[2])
z.min <- floor(z.range[1])
if(!is.null(zlim)) {
z.max <- max(z.max, ceiling(zlim[2] / z.scal))
z.min <- min(z.min, floor(zlim[1] / z.scal))
}
z.range <- range(z.min, z.max)
### init graphics
plot.new()
if(angle.2) {x1 <- x.min + yx.f * y.max; x2 <- x.max}
else {x1 <- x.min; x2 <- x.max + yx.f * y.max}
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
temp <- strwidth(format(rev(y.prty))[1], cex = cex.axis/par("cex"))
if(angle.2) x1 <- x1 - temp - y.margin.add
else x2 <- x2 + temp + y.margin.add
plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max))
if(angle > 2) par("usr" = par("usr")[c(2, 1, 3:4)])
usr <- par("usr") # we have to remind it for use in closures
title(main, sub, ...)
### draw axis, tick marks, labels, grid, ...
xx <- if(angle.2) c(x.min, x.max) else c(x.max, x.min)
if(grid) {
## grids
###################
# XY wall
i <- x.min:x.max;
segments(i, z.min, i + (yx.f * y.max), yz.f * y.max + z.min,
col = col.grid, lty = lty.grid);
i <- 0:y.max;
segments(x.min + (i * yx.f), i * yz.f + z.min,
x.max + (i * yx.f), i * yz.f + z.min,
col = col.grid, lty = lty.grid);
######################
# XZ wall
# verticle lines
temp <- yx.f * y.max;
temp1 <- yz.f * y.max;
i <- (x.min + temp):(x.max + temp);
segments(i, z.min + temp1, i, z.max + temp1,
col = col.grid, lty = lty.grid);
# horizontal lines
i <- (z.min + temp1):(z.max + temp1);
segments(x.min + temp, i, x.max + temp, i,
col = col.grid, lty = lty.grid)
##################
# YZ wall
# horizontal lines
i <- xx[2]:x.min;
mm <- z.min:z.max;
segments(i, mm, i + temp, mm + temp1,
col = col.grid, lty = lty.grid);
# verticle lines
i <- 0:y.max;
segments(x.min + (i * yx.f), i * yz.f + z.min,
xx[2] + (i * yx.f), i * yz.f + z.max,
col = col.grid, lty = lty.grid)
# make the axis into solid line
segments(x.min, z.min, x.min + (yx.f * y.max), yz.f * y.max + z.min,
col = col.grid, lty = lty.hide);
segments(x.max, z.min, x.max + (yx.f * y.max), yz.f * y.max + z.min,
col = col.axis, lty = lty.hide);
segments(x.min + (y.max * yx.f), y.max * yz.f + z.min,
x.max + (y.max* yx.f), y.max * yz.f + z.min,
col = col.grid, lty = lty.hide);
segments(x.min + temp, z.min + temp1, x.min + temp, z.max + temp1,
col = col.grid, lty = lty.hide);
segments(x.max + temp, z.min + temp1, x.max + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
segments(x.min + temp, z.max + temp1, x.max + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
segments(xx[2], z.max, xx[2] + temp, z.max + temp1,
col = col.axis, lty = lty.hide);
}
if(axis) {
if(tick.marks) { ## tick marks
xtl <- (z.max - z.min) * (tcl <- -par("tcl")) / 50
ztl <- (x.max - x.min) * tcl / 50
mysegs <- function(x0,y0, x1,y1)
segments(x0,y0, x1,y1, col=col.axis, lty=lty.axis)
## Y
i.y <- 0:y.max
mysegs(yx.f * i.y - ztl + xx[1], yz.f * i.y + z.min,
yx.f * i.y + ztl + xx[1], yz.f * i.y + z.min)
## X
i.x <- x.min:x.max
mysegs(i.x, -xtl + z.min, i.x, xtl + z.min)
## Z
i.z <- z.min:z.max
mysegs(-ztl + xx[2], i.z, ztl + xx[2], i.z)
if(label.tick.marks) { ## label tick marks
las <- par("las")
mytext <- function(labels, side, at, ...)
mtext(text = labels, side = side, at = at, line = -.5,
col=col.lab, cex=cex.axis, font=font.lab, ...)
## X
if(is.null(x.ticklabs))
x.ticklabs <- format(i.x * x.scal)
mytext(x.ticklabs, side = 1, at = i.x)
## Z
if(is.null(z.ticklabs))
z.ticklabs <- format(i.z * z.scal)
mytext(z.ticklabs, side = if(angle.1) 4 else 2, at = i.z,
adj = if(0 < las && las < 3) 1 else NA)
## Y
temp <- if(angle > 2) rev(i.y) else i.y ## turn y-labels around
if(is.null(y.ticklabs))
y.ticklabs <- format(y.prty)
else if (angle > 2)
y.ticklabs <- rev(y.ticklabs)
text(i.y * yx.f + xx[1],
i.y * yz.f + z.min, y.ticklabs,
pos=if(angle.1) 2 else 4, offset=1,
col=col.lab, cex=cex.axis/par("cex"), font=font.lab)
}
}
## axis and labels
mytext2 <- function(lab, side, line, at)
mtext(lab, side = side, line = line, at = at, col = col.lab,
cex = cex.lab, font = font.axis, las = 0)
## X
lines(c(x.min, x.max), c(z.min, z.min), col = col.axis, lty = lty.axis)
mytext2(xlab, 1, line = 1.5, at = mean(x.range))
## Y
lines(xx[1] + c(0, y.max * yx.f), c(z.min, y.max * yz.f + z.min),
col = col.axis, lty = lty.axis)
mytext2(ylab, if(angle.1) 2 else 4, line= 0.5, at = z.min + y.max * yz.f)
## Z
lines(xx[c(2,2)], c(z.min, z.max), col = col.axis, lty = lty.axis)
mytext2(zlab, if(angle.1) 4 else 2, line= 1.5, at = mean(z.range))
}
### plot points
x <- dat$x + (dat$y * yx.f)
z <- dat$z + (dat$y * yz.f)
col <- as.character(dat$col)
if(type == "h") {
z2 <- dat$y * yz.f + z.min
segments(x, z, x, z2, col = col, cex = cex.symbols, lty = lty.hplot, ...)
points(x, z, type = "p", col = col, pch = pch, cex = cex.symbols, ...)
}
else points(x, z, type = type, col = col, pch = pch, cex = cex.symbols, ...)
### box-lines in front of points (overlay)
if(axis && box) {
lines(c(x.min, x.max), c(z.max, z.max),
col = col.axis, lty = lty.axis)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max,
col = col.axis, lty = lty.axis)
lines(xx[c(1,1)], c(z.min, z.max), col = col.axis, lty = lty.axis)
}
# par(mem.par) # we MUST NOT set the margins back
### Return Function Object
ob <- ls() ## remove all unused objects from the result's enviroment:
rm(list = ob[!ob %in% c("angle", "mar", "usr", "x.scal", "y.scal", "z.scal", "yx.f",
"yz.f", "y.add", "z.min", "z.max", "x.min", "x.max", "y.max",
"x.prty", "y.prty", "z.prty")])
rm(ob)
invisible(list(
xyz.convert = function(x, y=NULL, z=NULL) {
xyz <- xyz.coords(x, y, z)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
}
y <- (xyz$y - y.add) / y.scal
return(list(x = xyz$x / x.scal + yx.f * y,
y = xyz$z / z.scal + yz.f * y))
},
points3d = function(x, y = NULL, z = NULL, type = "p", ...) {
xyz <- xyz.coords(x, y, z)
if(angle > 2) { ## switch y and x axis to ensure righthand oriented coord.
temp <- xyz$x; xyz$x <- xyz$y; xyz$y <- temp
}
y2 <- (xyz$y - y.add) / y.scal
x <- xyz$x / x.scal + yx.f * y2
y <- xyz$z / z.scal + yz.f * y2
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
if(type == "h") {
y2 <- z.min + yz.f * y2
segments(x, y, x, y2, ...)
points(x, y, type = "p", ...)
}
else points(x, y, type = type, ...)
},
plane3d = function(Intercept, x.coef = NULL, y.coef = NULL,
lty = "dashed", lty.box = NULL, ...){
if(!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept)
if(is.null(lty.box)) lty.box <- lty
if(is.null(x.coef) && length(Intercept) == 3){
x.coef <- Intercept[if(angle > 2) 3 else 2]
y.coef <- Intercept[if(angle > 2) 2 else 3]
Intercept <- Intercept[1]
}
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
x <- x.min:x.max
ltya <- c(lty.box, rep(lty, length(x)-2), lty.box)
x.coef <- x.coef * x.scal
z1 <- (Intercept + x * x.coef + y.add * y.coef) / z.scal
z2 <- (Intercept + x * x.coef +
(y.max * y.scal + y.add) * y.coef) / z.scal
segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max, lty = ltya, ...)
y <- 0:y.max
ltya <- c(lty.box, rep(lty, length(y)-2), lty.box)
y.coef <- (y * y.scal + y.add) * y.coef
z1 <- (Intercept + x.min * x.coef + y.coef) / z.scal
z2 <- (Intercept + x.max * x.coef + y.coef) / z.scal
segments(x.min + y * yx.f, z1 + y * yz.f,
x.max + y * yx.f, z2 + y * yz.f, lty = ltya, ...)
},
wall3d = function(Intercept, x.coef = NULL, y.coef = NULL,
lty = "dashed", lty.box = NULL, ...){
if(!is.atomic(Intercept) && !is.null(coef(Intercept))) Intercept <- coef(Intercept)
if(is.null(lty.box)) lty.box <- lty
if(is.null(x.coef) && length(Intercept) == 3){
x.coef <- Intercept[if(angle > 2) 3 else 2]
y.coef <- Intercept[if(angle > 2) 2 else 3]
Intercept <- Intercept[1]
}
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
x <- x.min:x.max
ltya <- c(lty.box, rep(lty, length(x)-2), lty.box)
x.coef <- x.coef * x.scal
z1 <- (Intercept + x * x.coef + y.add * y.coef) / z.scal
z2 <- (Intercept + x * x.coef +
(y.max * y.scal + y.add) * y.coef) / z.scal
segments(x, z1, x + y.max * yx.f, z2 + yz.f * y.max, lty = ltya, ...)
y <- 0:y.max
ltya <- c(lty.box, rep(lty, length(y)-2), lty.box)
y.coef <- (y * y.scal + y.add) * y.coef
z1 <- (Intercept + x.min * x.coef + y.coef) / z.scal
z2 <- (Intercept + x.max * x.coef + y.coef) / z.scal
segments(x.min + y * yx.f, z1 + y * yz.f,
x.max + y * yx.f, z2 + y * yz.f, lty = ltya, ...)
},
box3d = function(...){
mem.par <- par(mar = mar, usr = usr)
on.exit(par(mem.par))
lines(c(x.min, x.max), c(z.max, z.max), ...)
lines(c(0, y.max * yx.f) + x.max, c(0, y.max * yz.f) + z.max, ...)
lines(c(0, y.max * yx.f) + x.min, c(0, y.max * yz.f) + z.max, ...)
lines(c(x.max, x.max), c(z.min, z.max), ...)
lines(c(x.min, x.min), c(z.min, z.max), ...)
lines(c(x.min, x.max), c(z.min, z.min), ...)
}
))
}
#'Create 3D PCA score plot
#'@description This function creates both a static 3D PCA score plot as well as an interactive 3D PCA score plot
#'using the plotly R package. The 3D PCA score plot is stored in the mSetObj (mSetObj$imgSet$pca.3d). To view
#'the plot, if your mSetObj is named mSet, type "mSet$imgSet$pca.3d" inro your R console, and the 3D plot will appear.
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@usage PlotPCA3DScoreImg(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl)
#'@param mSetObj Input name of the created mSet Object.
#'@param imgName Input a name for the plot.
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@usage mSet <- PlotPCA3DScore(mSetObj=NA, imgName, format="json", dpi=72, width=NA, inx1, inx2, inx3, angl)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotPCA3DScoreImg <- function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
xlabel = paste("PC",inx1, "(", round(100*mSetObj$analSet$pca$variance[inx1],1), "%)");
ylabel = paste("PC",inx2, "(", round(100*mSetObj$analSet$pca$variance[inx2],1), "%)");
zlabel = paste("PC",inx3, "(", round(100*mSetObj$analSet$pca$variance[inx3],1), "%)");
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$pca.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
if(mSetObj$dataSet$cls.type == "disc"){
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
Plot3D(mSetObj$analSet$pca$x[, inx1], mSetObj$analSet$pca$x[, inx2], mSetObj$analSet$pca$x[, inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, color=cols, pch=pchs, box=F);
legend("topleft", legend =legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = mSetObj$analSet$pca$x[, inx1], y = mSetObj$analSet$pca$x[, inx2], z = mSetObj$analSet$pca$x[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$pca.3d <- p;
print("The Interactive 3D PCA plot has been created, please find it in mSet$imgSet$pca.3d.")
}
}else{
Plot3D(mSetObj$analSet$pca$x[, inx1], mSetObj$analSet$pca$x[, inx2], mSetObj$analSet$pca$x[, inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, pch=pchs, box=F);
dev.off();
if(!.on.public.web){
# 3D View using plotly
col <- c("#C61951", "#1972A4")
p <- plotly::plot_ly(x = mSetObj$analSet$pca$x[, inx1], y = mSetObj$analSet$pca$x[, inx2], z = mSetObj$analSet$pca$x[, inx3],
color = pchs, colors = col, marker = list(colorbar = list(len = 1, tickmode = array, tickvals = range(unique(pchs)),
ticktext = levels(mSetObj$dataSet$cls))));
p <- plotly::add_markers(p, sizes = 1000);
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)));
mSetObj$imgSet$pca.3d <- p;
print("The Interactive 3D PCA plot has been created, please find it in mSet$imgSet$pca.3d.")
}
}
return(.set.mSet(mSetObj));
}
#'Plot sPLS-DA 3D score plot
#'@description This function creates two 3D sPLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$splsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$splsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotSPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$spls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
spls3d <- list();
## need to check if only 2 or 3 components generated
if(length(mSetObj$analSet$splsr$explained_variance$X)==2){
spls3d$score$axis <- paste("Component", c(inx1, inx2), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2)], 5));
spls3d$score$axis <- c(spls3d$score$axis, "Component3 (NA)");
coords <- rbind(coords, "comp 3"=rep (0, ncol(coords)));
}else{
spls3d$score$axis <- paste("Component", c(inx1, inx2, inx3), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2, inx3)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2, inx3)], 5));
}
xlabel <- spls3d$score$axis[1]
ylabel <- spls3d$score$axis[2]
zlabel <- spls3d$score$axis[3]
# static
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(coords[,inx1], coords[,inx2], coords[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle = angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = coords[, inx1], y = coords[, inx2], z = coords[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$splsda.3d <- p;
print("The Interactive 3D sPLS-DA plot has been created, please find it in mSet$imgSet$splsda.3d.")
}
return(.set.mSet(mSetObj));
}
#'Plot sPLS-DA 3D score plot
#'@description This function creates two 3D sPLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$splsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$splsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotSPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$spls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
spls3d <- list();
## need to check if only 2 or 3 components generated
if(length(mSetObj$analSet$splsr$explained_variance$X)==2){
spls3d$score$axis <- paste("Component", c(inx1, inx2), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2)], 5));
spls3d$score$axis <- c(spls3d$score$axis, "Component3 (NA)");
coords <- rbind(coords, "comp 3"=rep (0, ncol(coords)));
}else{
spls3d$score$axis <- paste("Component", c(inx1, inx2, inx3), " (", round(100*mSetObj$analSet$splsr$explained_variance$X[c(inx1, inx2, inx3)], 1), "%)", sep="");
coords <- data.frame(signif(mSetObj$analSet$splsr$variates$X[,c(inx1, inx2, inx3)], 5));
}
xlabel <- spls3d$score$axis[1]
ylabel <- spls3d$score$axis[2]
zlabel <- spls3d$score$axis[3]
# static
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(coords[,inx1], coords[,inx2], coords[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle = angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = coords[, inx1], y = coords[, inx2], z = coords[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$splsda.3d <- p;
print("The Interactive 3D sPLS-DA plot has been created, please find it in mSet$imgSet$splsda.3d.")
}
return(.set.mSet(mSetObj));
}
#'Plot PLS 3D score plot
#'@description This function creates two 3D PLS-DA score plots, the first is static for Analysis Report purposes, as well as
#'an interactive 3D plot using the plotly R package. The 3D score plot is saved in the created mSetObj (mSetObj$imgSet$plsda.3d).
#'To view the score plot, if the name of your mSetObj is mSet, enter "mSet$imgSet$plsda.3d" to view the interactive score plot.
#'@param mSetObj Input name of the created mSet Object
#'@param imgName Input a name for the plot
#'@param format Select the image format, "png", or "pdf".
#'@param dpi Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images,
#'the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
#'@param width Input the width, there are 2 default widths, the first, width = NULL, is 10.5.
#'The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
#'@param inx1 Numeric, indicate the number of the principal component for the x-axis of the loading plot.
#'@param inx2 Numeric, indicate the number of the principal component for the y-axis of the loading plot.
#'@param inx3 Numeric, indicate the number of the principal component for the z-axis of the loading plot.
#'@param angl Input the angle
#'@author Jeff Xia\email{jeff.xia@mcgill.ca}
#'McGill University, Canada
#'License: GNU GPL (>= 2)
#'@export
#'@importFrom plotly plot_ly add_markers layout
PlotPLS3DScoreImg<-function(mSetObj=NA, imgName, format="png", dpi=72, width=NA, inx1, inx2, inx3, angl){
mSetObj <- .get.mSet(mSetObj);
imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
if(is.na(width)){
w <- 9;
}else if(width == 0){
w <- 7.2;
}else{
w <- width;
}
h <- w;
mSetObj$imgSet$pls.score3d <- imgName;
Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
par(mar=c(5,5,3,3));
xlabel <- paste("Component", inx1, "(", round(100*mSetObj$analSet$plsr$Xvar[inx1]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
ylabel <- paste("Component", inx2, "(", round(100*mSetObj$analSet$plsr$Xvar[inx2]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
zlabel <- paste("Component", inx3, "(", round(100*mSetObj$analSet$plsr$Xvar[inx3]/mSetObj$analSet$plsr$Xtotvar,1), "%)");
cols <- GetColorSchema(mSetObj);
legend.nm <- unique(as.character(mSetObj$dataSet$cls));
uniq.cols <- unique(cols);
pchs <- as.numeric(mSetObj$dataSet$cls)+1;
uniq.pchs <- unique(pchs);
Plot3D(mSetObj$analSet$plsr$score[,inx1], mSetObj$analSet$plsr$score[,inx2], mSetObj$analSet$plsr$score[,inx3], xlab= xlabel, ylab=ylabel,
zlab=zlabel, angle =angl, color=cols, pch=pchs, box=F);
legend("topleft", legend = legend.nm, pch=uniq.pchs, col=uniq.cols);
dev.off();
if(!.on.public.web){
# 3D View using plotly
if(length(uniq.pchs) > 3){
col <- RColorBrewer::brewer.pal(length(uniq.pchs), "Set3")
}else{
col <- c("#1972A4", "#FF7070")
}
p <- plotly::plot_ly(x = mSetObj$analSet$plsr$score[, inx1], y = mSetObj$analSet$plsr$score[, inx2], z = mSetObj$analSet$plsr$score[, inx3],
color = mSetObj$dataSet$cls, colors = col)
p <- plotly::add_markers(p, sizes = 5)
p <- plotly::layout(p, scene = list(xaxis = list(title = xlabel),
yaxis = list(title = ylabel),
zaxis = list(title = zlabel)))
mSetObj$imgSet$plsda.3d <- p;
print("The Interactive 3D PLS-DA plot has been created, please find it in mSet$imgSet$plsda.3d.")
}
return(.set.mSet(mSetObj));
}
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