R/bdm_qMap.R
In jgarriga65/bigMap: Big Data Mapping
Defines functions
bdm.pMap
qMap.plot1
bdm.qMap
Documented in
bdm.pMap
bdm.qMap
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# The bigMap Package for R.
# Copyright (c) 2018, Joan Garriga <jgarriga@ceab.csic.es>, Frederic Bartumeus <fbartu@ceab.csic.es> (Blanes Centre for Advanced Studies, CEAB-CSIC).
# bigMap is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
# bigMap is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses.
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#' ptSNE quantile-maps
#'
#' Maps quantitative variables onto the embedding space.
#'
#' @param data A \code{matrix/data.frame} to be mapped.
#'
#' @param bdm A \var{bdm} instance as generated by \code{bdm.init()}.
#'
#' @param labels A length \code{nrow(bdm$data)} vector of class labels to overlay onto the embedding. Label values are factorized as \var{as.numeric(as.factor(labels))}. Default value is \var{labels = NULL}.
#'
#' @param subset A numeric vector with the indexes of a subset of data. Data-points in the subset are heat-mapped and the rest are shown in light grey. By default all data-points are heat-mapped.
#'
#' @param qMap.levels The number of levels of the quantile-map (8 by default).
#'
#' @param qMap.cex The size of the data-points (as in \code{par()}).
#'
#' @param qMap.bg The background colour of the qMap plot. Default value is \code{ptsne.bg = #FFFFFF} (white).
#'
#' @param class.pltt If \code{!is.null(labels)} or \code{!is.null(bdm$lbls)}, a colour palette to show class labels with the qMap plots. By default (\code{qMap.pltt = NULL}) the default palette is used.
#'
#' @param qtitle A vector of strings with titles for the plots. Default value is \code{qtitle=NULL}.
#'
#' @param cex.main The font size of the title (as in \code{par()}).
#'
#' @param colorbar A logical value (TRUE by default). FALSE hides the side colorbar.
#'
#' @param layer The number of a layer (1 by default).
#'
#' @return None.
#'
#' @details This is not a heat-map but a quantile-map plot. This function splits the range of each variable into as many quantiles as specified by \var{levels} so that the color gradient will hardly ever correspond to a constant numeric gradient. Thus, the mapping will show more evenly distributed colors though at the expense of possibly exaggerating artifacts. For variables with very extrem distributions, it will be impossible to find as many quantiles as desired and the distribution of colors will not be so homogeneous.
#' @examples
#'
#' bdm.example()
#' bdm.qMap(ex$map, ex$data)
#' # --- show only components (1, 2, 4, 8) of the GMM
#' bdm.qMap(ex$map, ex$data, subset = which(ex$map$lbls %in% c(1, 4, 8, 16)))
bdm.qMap <- function(bdm, data, labels = NULL, subset = NULL, qMap.levels = 8, qMap.cex = 0.3, qMap.bg = '#FFFFFF', class.pltt = NULL, qtitle =NULL, cex.main = 1.0, colorbar = T, layer = 1)
{
# get data
if (is.null(data))
return(message('+++ Error: no data given !'))
# check 1 single plot
if (is.null(ncol(data))){
qMap.plot1(bdm, as.numeric(data), qMap.levels = qMap.levels, qMap.cex = qMap.cex, qMap.bg = qMap.bg, qtitle = qtitle, cex.main = cex.main, colorbar = colorbar)
return()
}
# get labels
if (!is.null(labels)) labels <- as.numeric(as.factor(labels))
# get var names
if (is.null(colnames(data))) {
colnames(data) <- paste('V', formatC(seq(ncol(data)), width = 2, flag = '0'), sep = '.')
}
# join labels & data
if (!is.null(labels)) data <- cbind(labels, data)
# check number of vars
if (ncol(data) > 20) {
data <- data[, 1:20]
cat('+++ WARNING: plotting first ', ncol(data) - !is.null(labels), ' columns !, \n', sep='')
}
# get mapping
l <- c(1, 2) + (layer -1) *2
Y <- bdm$ptsne$Y[ , l]
# set graphic environment (Att!! with this)
if (colorbar)
{
layout.mtx <- t(cbind(layout.get(ncol(data)), layout.get(ncol(data))))
layout.mtx[ , ] <- seq(length(layout.mtx))
layout.mtx <- t(layout.mtx)
layout(layout.mtx, widths = rep(2 /ncol(layout.mtx) *c(0.73, 0.27), ncol(layout.mtx)))
} else
{
layout.mtx <- layout.get(ncol(data))
layout.mtx[ , ] <- seq(length(layout.mtx))
layout.mtx <- t(layout.mtx)
layout(layout.mtx)
}
c1 <- c(4.5, 3.5, 2.5, 1.5, 0.5)
c3 <- c(8, 7, 6, 5, 4)
parbdm.set(oma = c(c1[nrow(layout.mtx)], 1, c3[nrow(layout.mtx)], 1))
# legend palette
hmap.pltt <- c(pltt.heat(qMap.levels), '#DDDDDDFF')
nulL <- lapply(seq(ncol(data)), function(j){
if (j == 1 & !is.null(labels)) {
X <- data[, j]
if (is.null(class.pltt))
pltt <- c(pltt.get(s = length(unique(X))), '#DDDDDDFF')
else
pltt <- class.pltt
}
else {
# factor data
X <- get.lvls(data[, j], qMap.levels)
Q <- quantile(data[, j][!is.na(data[, j])], seq(0, 1, length.out = qMap.levels+1))
pltt <- hmap.pltt
}
# plot q-maps
par(mar = c(1.0, 1.0, 0.8, 0.4))
if (!is.null(subset)) {
# plot shadow
plot(Y[-subset, ], xaxt = 'n', xlab = '', yaxt = 'n', ylab = '', xlim = range(Y[,1]), ylim = range(Y[,2]), col = pltt[length(pltt)], cex = qMap.cex, pch = 20, asp = 1, main = colnames(data)[j], cex.main = cex.main)
# plot subset q-map
points(Y[subset, ], col = pltt[X[subset]], cex = qMap.cex, pch = 20, asp = 1)
}
else {
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = qMap.cex, pch = 20, asp = 1, main = colnames(data)[j], cex.main = cex.main)
}
# plot title
# title(colnames(data)[j], line = 1.0, outer = T, cex.sub = 0.8)
# mtext(colnames(data)[j], side = 3, line = 2.0, at = 1.1 *min(Y[, 1]), cex = 1.0, pos = 'right')
# text(0.8 *min(Y[, 1]), 0.9 *max(Y[, 2]), labels = colnames(data)[j], cex = 1.0)
# plot legend
if (colorbar)
{
par(mar = c(1, 0.1, 0.5, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
if (j == 1 & !is.null(labels)) {
s <- length(unique(labels))
lgnd.lbls <- formatC(seq(s), width = 3)
legend('center', legend = lgnd.lbls[s:1], bty = 'n', pch = 15, cex = 0.6, pt.cex = 1.6, y.intersp = 0.7, col = pltt[s:1])
} else {
lgnd.lbls <- sapply(seq(qMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[qMap.levels:1], bty = 'n', pch = 15, cex = 0.6, pt.cex = 1.6, y.intersp = 0.7, col = pltt[qMap.levels:1])
}
}
})
# fill layout
if (length(ncol(data)) < max(layout.get(length(ncol(data))))) plot.null()
# layout title
if (is.null(qtitle)) qtitle <- bdm$dSet
title(qtitle, outer = T, cex.main = 1.0)
# reset graphic environment
parbdm.def()
}
qMap.plot1 <- function(bdm, data, qMap.levels = 8, qMap.cex = 0.3, qMap.bg = '#FFFFFF', qtitle =NULL, cex.main = 1.0, colorbar = T)
{
# get data
if (is.null(data))
return(message('+++ Error: no data given !'))
# get mapping
Y <- bdm$ptsne$Y[ , 1:2]
# set graphic environment (Att!! with this)
if (colorbar) layout(matrix(1:2, nrow = 1), widths = c(0.73, 0.27))
parbdm.set(oma = c(0.5, 0.5, 2.0, 0.5))
# legend palette
hmap.pltt <- c(pltt.heat(qMap.levels), '#DDDDDDFF')
# factor data
X <- get.lvls(data, qMap.levels)
Q <- quantile(data[!is.na(data)], seq(0, 1, length.out = qMap.levels+1))
pltt <- hmap.pltt
par(mar = c(1.0, 1.0, 2.0, 0.4))
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = qMap.cex, pch = 20, asp = 1, main = qtitle, cex.main = cex.main)
# plot legend
if (colorbar)
{
par(mar = c(1, 0.1, 2.0, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
lgnd.lbls <- sapply(seq(qMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[qMap.levels:1], bty = 'n', pch = 15, cex = 1.0, pt.cex = 2.0, y.intersp = 1.0, col = pltt[qMap.levels:1])
}
# reset graphic environment
parbdm.def()
}
#' Precision map (quantile map of betas)
#'
#' @param bdm A \var{bdm} instance as generated by \code{bdm.init()}.
#'
#' @param pMap.levels The number of levels of the quantile-map (8 by default).
#'
#' @param pMap.cex The size of the data-points (as in \code{par()}). Default value is \code{ptsne.cex = 0.1}.
#'
#' @param pMap.bg The background colour of the qMap plot. Default value is \code{ptsne.bg = #FFFFFF} (white).
#'
#' @param colorbar A logical value (TRUE by default). FALSE hides the side colorbar.
#'
#' @return None.
#'
#' @examples
#'
#' bdm.example()
#' bdm.pMap(ex$map)
bdm.pMap <- function(bdm, pMap.levels = 8, pMap.cex = 0.1, pMap.bg = '#000000', colorbar = T)
{
# get mapping
Y <- bdm$ptsne$Y[, 1:2]
# legend palette
if (pMap.bg == '#000000')
pltt <- c(pltt.heat(pMap.levels), '#DDDDDD')
else
pltt <- c(pltt.heat(pMap.levels), '#000000')
#factor data
data <- bdm$ppx$B[, 1]
X <- get.lvls(data, pMap.levels)
Q <- quantile(data, seq(0, 1, length.out = pMap.levels+1))
# set graphic environment
parbdm.set(oma = c(1.0, 1.0, 1.0, 1.0), mar = c(1.0, 1.0, 0.2, 0.4), bg = pMap.bg)
layout(matrix(seq(2), nrow = 1), widths = c(0.73, 0.27))
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', bty = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = pMap.cex, pch = 20, asp = 1)
# plot legend
if (colorbar)
{
par(mar = c(1.0, 0.1, 0.2, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
lgnd.lbls <- sapply(seq(pMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[pMap.levels:1], bty = 'n', pch = 15, cex = 1.2, pt.cex = 1.2, y.intersp = 1.1, col = pltt[pMap.levels:1], text.col = pltt[length(pltt)])
}
# reset graphic environment
parbdm.def()
}
jgarriga65/bigMap documentation built on June 10, 2024, 7:05 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions bdm.pMap qMap.plot1 bdm.qMap
Documented in bdm.pMap bdm.qMap
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# The bigMap Package for R.
# Copyright (c) 2018, Joan Garriga <jgarriga@ceab.csic.es>, Frederic Bartumeus <fbartu@ceab.csic.es> (Blanes Centre for Advanced Studies, CEAB-CSIC).
# bigMap is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
# bigMap is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses.
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#' ptSNE quantile-maps
#'
#' Maps quantitative variables onto the embedding space.
#'
#' @param data A \code{matrix/data.frame} to be mapped.
#'
#' @param bdm A \var{bdm} instance as generated by \code{bdm.init()}.
#'
#' @param labels A length \code{nrow(bdm$data)} vector of class labels to overlay onto the embedding. Label values are factorized as \var{as.numeric(as.factor(labels))}. Default value is \var{labels = NULL}.
#'
#' @param subset A numeric vector with the indexes of a subset of data. Data-points in the subset are heat-mapped and the rest are shown in light grey. By default all data-points are heat-mapped.
#'
#' @param qMap.levels The number of levels of the quantile-map (8 by default).
#'
#' @param qMap.cex The size of the data-points (as in \code{par()}).
#'
#' @param qMap.bg The background colour of the qMap plot. Default value is \code{ptsne.bg = #FFFFFF} (white).
#'
#' @param class.pltt If \code{!is.null(labels)} or \code{!is.null(bdm$lbls)}, a colour palette to show class labels with the qMap plots. By default (\code{qMap.pltt = NULL}) the default palette is used.
#'
#' @param qtitle A vector of strings with titles for the plots. Default value is \code{qtitle=NULL}.
#'
#' @param cex.main The font size of the title (as in \code{par()}).
#'
#' @param colorbar A logical value (TRUE by default). FALSE hides the side colorbar.
#'
#' @param layer The number of a layer (1 by default).
#'
#' @return None.
#'
#' @details This is not a heat-map but a quantile-map plot. This function splits the range of each variable into as many quantiles as specified by \var{levels} so that the color gradient will hardly ever correspond to a constant numeric gradient. Thus, the mapping will show more evenly distributed colors though at the expense of possibly exaggerating artifacts. For variables with very extrem distributions, it will be impossible to find as many quantiles as desired and the distribution of colors will not be so homogeneous.
#' @examples
#'
#' bdm.example()
#' bdm.qMap(ex$map, ex$data)
#' # --- show only components (1, 2, 4, 8) of the GMM
#' bdm.qMap(ex$map, ex$data, subset = which(ex$map$lbls %in% c(1, 4, 8, 16)))
bdm.qMap <- function(bdm, data, labels = NULL, subset = NULL, qMap.levels = 8, qMap.cex = 0.3, qMap.bg = '#FFFFFF', class.pltt = NULL, qtitle =NULL, cex.main = 1.0, colorbar = T, layer = 1)
{
# get data
if (is.null(data))
return(message('+++ Error: no data given !'))
# check 1 single plot
if (is.null(ncol(data))){
qMap.plot1(bdm, as.numeric(data), qMap.levels = qMap.levels, qMap.cex = qMap.cex, qMap.bg = qMap.bg, qtitle = qtitle, cex.main = cex.main, colorbar = colorbar)
return()
}
# get labels
if (!is.null(labels)) labels <- as.numeric(as.factor(labels))
# get var names
if (is.null(colnames(data))) {
colnames(data) <- paste('V', formatC(seq(ncol(data)), width = 2, flag = '0'), sep = '.')
}
# join labels & data
if (!is.null(labels)) data <- cbind(labels, data)
# check number of vars
if (ncol(data) > 20) {
data <- data[, 1:20]
cat('+++ WARNING: plotting first ', ncol(data) - !is.null(labels), ' columns !, \n', sep='')
}
# get mapping
l <- c(1, 2) + (layer -1) *2
Y <- bdm$ptsne$Y[ , l]
# set graphic environment (Att!! with this)
if (colorbar)
{
layout.mtx <- t(cbind(layout.get(ncol(data)), layout.get(ncol(data))))
layout.mtx[ , ] <- seq(length(layout.mtx))
layout.mtx <- t(layout.mtx)
layout(layout.mtx, widths = rep(2 /ncol(layout.mtx) *c(0.73, 0.27), ncol(layout.mtx)))
} else
{
layout.mtx <- layout.get(ncol(data))
layout.mtx[ , ] <- seq(length(layout.mtx))
layout.mtx <- t(layout.mtx)
layout(layout.mtx)
}
c1 <- c(4.5, 3.5, 2.5, 1.5, 0.5)
c3 <- c(8, 7, 6, 5, 4)
parbdm.set(oma = c(c1[nrow(layout.mtx)], 1, c3[nrow(layout.mtx)], 1))
# legend palette
hmap.pltt <- c(pltt.heat(qMap.levels), '#DDDDDDFF')
nulL <- lapply(seq(ncol(data)), function(j){
if (j == 1 & !is.null(labels)) {
X <- data[, j]
if (is.null(class.pltt))
pltt <- c(pltt.get(s = length(unique(X))), '#DDDDDDFF')
else
pltt <- class.pltt
}
else {
# factor data
X <- get.lvls(data[, j], qMap.levels)
Q <- quantile(data[, j][!is.na(data[, j])], seq(0, 1, length.out = qMap.levels+1))
pltt <- hmap.pltt
}
# plot q-maps
par(mar = c(1.0, 1.0, 0.8, 0.4))
if (!is.null(subset)) {
# plot shadow
plot(Y[-subset, ], xaxt = 'n', xlab = '', yaxt = 'n', ylab = '', xlim = range(Y[,1]), ylim = range(Y[,2]), col = pltt[length(pltt)], cex = qMap.cex, pch = 20, asp = 1, main = colnames(data)[j], cex.main = cex.main)
# plot subset q-map
points(Y[subset, ], col = pltt[X[subset]], cex = qMap.cex, pch = 20, asp = 1)
}
else {
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = qMap.cex, pch = 20, asp = 1, main = colnames(data)[j], cex.main = cex.main)
}
# plot title
# title(colnames(data)[j], line = 1.0, outer = T, cex.sub = 0.8)
# mtext(colnames(data)[j], side = 3, line = 2.0, at = 1.1 *min(Y[, 1]), cex = 1.0, pos = 'right')
# text(0.8 *min(Y[, 1]), 0.9 *max(Y[, 2]), labels = colnames(data)[j], cex = 1.0)
# plot legend
if (colorbar)
{
par(mar = c(1, 0.1, 0.5, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
if (j == 1 & !is.null(labels)) {
s <- length(unique(labels))
lgnd.lbls <- formatC(seq(s), width = 3)
legend('center', legend = lgnd.lbls[s:1], bty = 'n', pch = 15, cex = 0.6, pt.cex = 1.6, y.intersp = 0.7, col = pltt[s:1])
} else {
lgnd.lbls <- sapply(seq(qMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[qMap.levels:1], bty = 'n', pch = 15, cex = 0.6, pt.cex = 1.6, y.intersp = 0.7, col = pltt[qMap.levels:1])
}
}
})
# fill layout
if (length(ncol(data)) < max(layout.get(length(ncol(data))))) plot.null()
# layout title
if (is.null(qtitle)) qtitle <- bdm$dSet
title(qtitle, outer = T, cex.main = 1.0)
# reset graphic environment
parbdm.def()
}
qMap.plot1 <- function(bdm, data, qMap.levels = 8, qMap.cex = 0.3, qMap.bg = '#FFFFFF', qtitle =NULL, cex.main = 1.0, colorbar = T)
{
# get data
if (is.null(data))
return(message('+++ Error: no data given !'))
# get mapping
Y <- bdm$ptsne$Y[ , 1:2]
# set graphic environment (Att!! with this)
if (colorbar) layout(matrix(1:2, nrow = 1), widths = c(0.73, 0.27))
parbdm.set(oma = c(0.5, 0.5, 2.0, 0.5))
# legend palette
hmap.pltt <- c(pltt.heat(qMap.levels), '#DDDDDDFF')
# factor data
X <- get.lvls(data, qMap.levels)
Q <- quantile(data[!is.na(data)], seq(0, 1, length.out = qMap.levels+1))
pltt <- hmap.pltt
par(mar = c(1.0, 1.0, 2.0, 0.4))
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = qMap.cex, pch = 20, asp = 1, main = qtitle, cex.main = cex.main)
# plot legend
if (colorbar)
{
par(mar = c(1, 0.1, 2.0, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
lgnd.lbls <- sapply(seq(qMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[qMap.levels:1], bty = 'n', pch = 15, cex = 1.0, pt.cex = 2.0, y.intersp = 1.0, col = pltt[qMap.levels:1])
}
# reset graphic environment
parbdm.def()
}
#' Precision map (quantile map of betas)
#'
#' @param bdm A \var{bdm} instance as generated by \code{bdm.init()}.
#'
#' @param pMap.levels The number of levels of the quantile-map (8 by default).
#'
#' @param pMap.cex The size of the data-points (as in \code{par()}). Default value is \code{ptsne.cex = 0.1}.
#'
#' @param pMap.bg The background colour of the qMap plot. Default value is \code{ptsne.bg = #FFFFFF} (white).
#'
#' @param colorbar A logical value (TRUE by default). FALSE hides the side colorbar.
#'
#' @return None.
#'
#' @examples
#'
#' bdm.example()
#' bdm.pMap(ex$map)
bdm.pMap <- function(bdm, pMap.levels = 8, pMap.cex = 0.1, pMap.bg = '#000000', colorbar = T)
{
# get mapping
Y <- bdm$ptsne$Y[, 1:2]
# legend palette
if (pMap.bg == '#000000')
pltt <- c(pltt.heat(pMap.levels), '#DDDDDD')
else
pltt <- c(pltt.heat(pMap.levels), '#000000')
#factor data
data <- bdm$ppx$B[, 1]
X <- get.lvls(data, pMap.levels)
Q <- quantile(data, seq(0, 1, length.out = pMap.levels+1))
# set graphic environment
parbdm.set(oma = c(1.0, 1.0, 1.0, 1.0), mar = c(1.0, 1.0, 0.2, 0.4), bg = pMap.bg)
layout(matrix(seq(2), nrow = 1), widths = c(0.73, 0.27))
# plot q-map
plot(Y, xaxt = 'n', yaxt = 'n', bty = 'n', xlab = '', ylab = '', xlim = range(Y[, 1]), ylim = range(Y[, 2]), col = pltt[X], cex = pMap.cex, pch = 20, asp = 1)
# plot legend
if (colorbar)
{
par(mar = c(1.0, 0.1, 0.2, 0.1))
plot(1, 1, xlab = '', ylab = '', xaxt = "n", yaxt = "n", bty = "n", type = "n")
lgnd.lbls <- sapply(seq(pMap.levels), function(l) {
if (l == 1 || Q[l] != Q[l-1]) {
formatC(Q[l], format = 'e', digits = 2)
} else {
' '
}
})
legend('center', legend = lgnd.lbls[pMap.levels:1], bty = 'n', pch = 15, cex = 1.2, pt.cex = 1.2, y.intersp = 1.1, col = pltt[pMap.levels:1], text.col = pltt[length(pltt)])
}
# reset graphic environment
parbdm.def()
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.