R/Plot_DiffusionMap.R
In ChenWeiyan/LandSCENT: Landscape Single Cell Entropy
Defines functions
Plot_DiffusionMap
Documented in
Plot_DiffusionMap
#' @title
#' Visualize diffusion map
#'
#' @aliases Plot_DiffusionMap
#'
#' @description
#' This function visualizes the diffusion map in 2D or 3D plots
#'
#' @param Integration.l
#' Typically, it is the output from \code{DoDiffusionMap} function
#'
#' @param dim
#' A numeric vector. Diffusin components order in the plot axes. And
#' the sign of evrey entry indicates the direction of component.
#' Default is c(1, 2, 3)
#'
#' @param color_by
#' Indicating the variable used for coloring. \code{SR}
#' means the plot is colored by SR values. \code{DPT}
#' means the plot is colored by diffusion pseudotime
#'
#' @param TIPs
#' Specifying which trajectory paths should be shown on the
#' diffusion maps. Only available in 2D plot and when
#' \code{color_by} was set to be \code{DPT}
#'
#' @param phi
#' The angles defining the viewing direction. \code{phi}
#' gives the colatitude. Default is 20
#'
#' @param theta
#' The angles defining the viewing direction. \code{theta}
#' gives the azimuthal direction. Default is 40
#'
#' @param bty
#' The type of the box, the default \code{g} draws grey
#' background with white grid lines.
#' Note: the bty = "f", "b", "b2", "bl" can also be specified
#' for this argument
#'
#' @param ...
#' Additional arguments passed to the 3D plotting methods
#'
#' @param PDF
#' A logical. Output figure via pdf file or not, default is FALSE
#'
#' @return A pdf file contains the generated figure or a ggplot object
#'
#' @references
#' Teschendorff AE, Tariq Enver.
#' \emph{Single-cell entropy for accurate estimation of differentiation
#' potency from a cell’s transcriptome.}
#' Nature communications 8 (2017): 15599.
#' doi:\href{https://doi.org/10.1038/ncomms15599}{
#' 10.1038/ncomms15599}.
#'
#' Teschendorff, Andrew E., Peter Sollich, and Reimer Kuehn.
#' \emph{Signalling entropy: A novel network-theoretical framework
#' for systems analysis and interpretation of functional omic data.}
#' Methods 67.3 (2014): 282-293.
#' doi:\href{https://doi.org/10.1016/j.ymeth.2014.03.013}{
#' 10.1016/j.ymeth.2014.03.013}.
#'
#' @examples
#' \dontrun{
#' data(Example.m)
#' data(net13Jun12.m)
#' Integration.l <- DoIntegPPI(exp.m = Example.m[, c(1:58,61:84,86:98,100)], ppiA.m = net13Jun12.m)
#' data(SR.v)
#' Integration.l$SR <- SR.v
#' InferPotency.o <- InferPotency(Integration.l)
#' DoDM.o <- DoDiffusionMap(InferPotency.o)
#' Plot_DiffusionMap(DoDM.o)
#' }
#'
#' @import ggplot2
#' @import plot3D
#' @importFrom destiny DPT
#' @importFrom destiny plot
#' @importFrom ggthemes geom_rangeframe
#' @importFrom marray maPalette
#' @export
#'
Plot_DiffusionMap <- function(Integration.l,
dim = c(1, 2, 3),
color_by = c("SR", "DPT"),
TIPs = c(1, 2, 3),
phi = 20,
theta = 40,
bty = "g",
...,
PDF = FALSE){
dm <- Integration.l$DM
dms <- Integration.l$DMEigen
root.idx <- Integration.l$root
dpt <- destiny::DPT(dm, tips = Integration.l$root)
terminel.idx <- which(dpt@tips[,1])
term.idx <- terminel.idx[which(terminel.idx != root.idx)]
sign_dim <- sign(dim)
dcs <- dim
dim <- abs(dim)
DIMS <- max(dim)
DIM_dms <- dim(dms)[2]
if (DIMS > DIM_dms) {
stop("Diffusion map object does not contain enough dimensions, please reset dim argument!")
}
if (length(color_by) > 1) {
print("Specified more than one type of color, using the first type instead!")
color_by <- color_by[1]
}
colSR <- marray::maPalette(low="lightblue",
mid="skyblue",
high="darkblue",
k = 30)
colDPT <- marray::maPalette(low="#ffffb2",
mid="#fd8d3c",
high="#b10026",
k = 30)
point.SR <- "#d73027"
point.DPT <- "#3690c0"
if (color_by == "SR") {
color.idx <- Integration.l$SR
color.lab <- "SR"
panel.text <- "Diffusion Map Colored by SR Values"
colimage <- colSR
point.col <- point.SR
}else{
color.idx <- dpt[["dpt"]]
color.lab <- "DPT"
panel.text <- "Diffusion Map Colored by DPT Estimation"
colimage <- colDPT
point.col <- point.DPT
}
labs <- colnames(dms)[dim]
DIMS <- length(dim)
font.size <- 3.5
if (DIMS > 3) {
stop("dim is of wrong length: Can only handle 2 or 3 dimensions!")
}
if (PDF) {
pdf("DiffusionMap.pdf")
par(mar = c(2,2,2,2))
if (DIMS == 2) {
if (color_by == "SR") {
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- ggplot(dms, aes((sign_dim[1]*dms[, dim[1]]), (sign_dim[2]*dms[, dim[2]]), color = color.idx)) +
geom_point() +
xlab(labs[1]) +
ylab(labs[2]) +
labs(title = panel.text, color = color.lab) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
annotate("point", x = (sign_dim[1]*dms[terminel.idx, dim[1]]),
y = (sign_dim[2]*dms[terminel.idx, dim[2]]),
pch = 20, colour = "red", size = rel(3)) +
scale_color_gradientn(colors = c("lightblue", "skyblue", "darkblue")) +
theme_minimal() +
theme(legend.position = "right",
panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5),
axis.text = element_blank())+
ggthemes::geom_rangeframe(colour = par("col"))
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- destiny::plot(dpt, dcs = dcs, paths_to = TIPs) +
labs(title = panel.text, color = color.lab) +
xlab(labs[1]) +
ylab(labs[2]) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
theme(panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5))
}
print(g)
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
points3D(x = (sign_dim[1]*dms[, dim[1]]),
y = (sign_dim[2]*dms[, dim[2]]),
z = (sign_dim[3]*dms[, dim[3]]),
colvar = color.idx,
col = colimage,
colkey = list(length = 0.3),
phi = phi, theta = theta,
xlab = labs[1],
ylab = labs[2],
zlab = labs[3],
clab = color.lab,
pch = 20,
main = panel.text,
bty = bty,
...)
points3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
col = point.col,
pch = 2,
cex = 1.5,
plot = TRUE,
add = TRUE)
points3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
col = point.col,
pch = 5,
cex = 1.5,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
labels = rep(" Predicted\n Terminal\n Cell",
length(term.idx)),
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
labels = " Root Cell",
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
}
dev.off()
}else{
if (DIMS == 2) {
if (color_by == "SR") {
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- ggplot(dms, aes((sign_dim[1]*dms[, dim[1]]), (sign_dim[2]*dms[, dim[2]]), color = color.idx)) +
geom_point() +
xlab(labs[1]) +
ylab(labs[2]) +
labs(title = panel.text, color = color.lab) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
annotate("point", x = (sign_dim[1]*dms[terminel.idx, dim[1]]),
y = (sign_dim[2]*dms[terminel.idx, dim[2]]),
pch = 20, colour = "red", size = rel(3)) +
scale_color_gradientn(colors = c("lightblue", "skyblue", "darkblue")) +
theme_minimal() +
theme(legend.position = "right",
panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5),
axis.text = element_blank())+
ggthemes::geom_rangeframe(colour = par("col"))
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- destiny::plot(dpt, dcs = dcs, paths_to = TIPs) +
labs(title = panel.text, color = color.lab) +
xlab(labs[1]) +
ylab(labs[2]) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
theme(panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5))
}
print(g)
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
points3D(x = (sign_dim[1]*dms[, dim[1]]),
y = (sign_dim[2]*dms[, dim[2]]),
z = (sign_dim[3]*dms[, dim[3]]),
colvar = color.idx,
col = colimage,
colkey = list(length = 0.3),
phi = phi, theta = theta,
xlab = labs[1],
ylab = labs[2],
zlab = labs[3],
clab = color.lab,
pch = 20,
main = panel.text,
bty = bty,
...)
points3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
col = point.col,
pch = 2,
cex = 1.5,
plot = TRUE,
add = TRUE)
points3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
col = point.col,
pch = 5,
cex = 1.5,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
labels = rep(" Predicted\n Terminal\n Cell",
length(term.idx)),
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
labels = " Root Cell",
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
}
}
}
ChenWeiyan/LandSCENT documentation built on Aug. 28, 2020, 9:55 p.m.
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Defines functions Plot_DiffusionMap
Documented in Plot_DiffusionMap
#' @title
#' Visualize diffusion map
#'
#' @aliases Plot_DiffusionMap
#'
#' @description
#' This function visualizes the diffusion map in 2D or 3D plots
#'
#' @param Integration.l
#' Typically, it is the output from \code{DoDiffusionMap} function
#'
#' @param dim
#' A numeric vector. Diffusin components order in the plot axes. And
#' the sign of evrey entry indicates the direction of component.
#' Default is c(1, 2, 3)
#'
#' @param color_by
#' Indicating the variable used for coloring. \code{SR}
#' means the plot is colored by SR values. \code{DPT}
#' means the plot is colored by diffusion pseudotime
#'
#' @param TIPs
#' Specifying which trajectory paths should be shown on the
#' diffusion maps. Only available in 2D plot and when
#' \code{color_by} was set to be \code{DPT}
#'
#' @param phi
#' The angles defining the viewing direction. \code{phi}
#' gives the colatitude. Default is 20
#'
#' @param theta
#' The angles defining the viewing direction. \code{theta}
#' gives the azimuthal direction. Default is 40
#'
#' @param bty
#' The type of the box, the default \code{g} draws grey
#' background with white grid lines.
#' Note: the bty = "f", "b", "b2", "bl" can also be specified
#' for this argument
#'
#' @param ...
#' Additional arguments passed to the 3D plotting methods
#'
#' @param PDF
#' A logical. Output figure via pdf file or not, default is FALSE
#'
#' @return A pdf file contains the generated figure or a ggplot object
#'
#' @references
#' Teschendorff AE, Tariq Enver.
#' \emph{Single-cell entropy for accurate estimation of differentiation
#' potency from a cell’s transcriptome.}
#' Nature communications 8 (2017): 15599.
#' doi:\href{https://doi.org/10.1038/ncomms15599}{
#' 10.1038/ncomms15599}.
#'
#' Teschendorff, Andrew E., Peter Sollich, and Reimer Kuehn.
#' \emph{Signalling entropy: A novel network-theoretical framework
#' for systems analysis and interpretation of functional omic data.}
#' Methods 67.3 (2014): 282-293.
#' doi:\href{https://doi.org/10.1016/j.ymeth.2014.03.013}{
#' 10.1016/j.ymeth.2014.03.013}.
#'
#' @examples
#' \dontrun{
#' data(Example.m)
#' data(net13Jun12.m)
#' Integration.l <- DoIntegPPI(exp.m = Example.m[, c(1:58,61:84,86:98,100)], ppiA.m = net13Jun12.m)
#' data(SR.v)
#' Integration.l$SR <- SR.v
#' InferPotency.o <- InferPotency(Integration.l)
#' DoDM.o <- DoDiffusionMap(InferPotency.o)
#' Plot_DiffusionMap(DoDM.o)
#' }
#'
#' @import ggplot2
#' @import plot3D
#' @importFrom destiny DPT
#' @importFrom destiny plot
#' @importFrom ggthemes geom_rangeframe
#' @importFrom marray maPalette
#' @export
#'
Plot_DiffusionMap <- function(Integration.l,
dim = c(1, 2, 3),
color_by = c("SR", "DPT"),
TIPs = c(1, 2, 3),
phi = 20,
theta = 40,
bty = "g",
...,
PDF = FALSE){
dm <- Integration.l$DM
dms <- Integration.l$DMEigen
root.idx <- Integration.l$root
dpt <- destiny::DPT(dm, tips = Integration.l$root)
terminel.idx <- which(dpt@tips[,1])
term.idx <- terminel.idx[which(terminel.idx != root.idx)]
sign_dim <- sign(dim)
dcs <- dim
dim <- abs(dim)
DIMS <- max(dim)
DIM_dms <- dim(dms)[2]
if (DIMS > DIM_dms) {
stop("Diffusion map object does not contain enough dimensions, please reset dim argument!")
}
if (length(color_by) > 1) {
print("Specified more than one type of color, using the first type instead!")
color_by <- color_by[1]
}
colSR <- marray::maPalette(low="lightblue",
mid="skyblue",
high="darkblue",
k = 30)
colDPT <- marray::maPalette(low="#ffffb2",
mid="#fd8d3c",
high="#b10026",
k = 30)
point.SR <- "#d73027"
point.DPT <- "#3690c0"
if (color_by == "SR") {
color.idx <- Integration.l$SR
color.lab <- "SR"
panel.text <- "Diffusion Map Colored by SR Values"
colimage <- colSR
point.col <- point.SR
}else{
color.idx <- dpt[["dpt"]]
color.lab <- "DPT"
panel.text <- "Diffusion Map Colored by DPT Estimation"
colimage <- colDPT
point.col <- point.DPT
}
labs <- colnames(dms)[dim]
DIMS <- length(dim)
font.size <- 3.5
if (DIMS > 3) {
stop("dim is of wrong length: Can only handle 2 or 3 dimensions!")
}
if (PDF) {
pdf("DiffusionMap.pdf")
par(mar = c(2,2,2,2))
if (DIMS == 2) {
if (color_by == "SR") {
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- ggplot(dms, aes((sign_dim[1]*dms[, dim[1]]), (sign_dim[2]*dms[, dim[2]]), color = color.idx)) +
geom_point() +
xlab(labs[1]) +
ylab(labs[2]) +
labs(title = panel.text, color = color.lab) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
annotate("point", x = (sign_dim[1]*dms[terminel.idx, dim[1]]),
y = (sign_dim[2]*dms[terminel.idx, dim[2]]),
pch = 20, colour = "red", size = rel(3)) +
scale_color_gradientn(colors = c("lightblue", "skyblue", "darkblue")) +
theme_minimal() +
theme(legend.position = "right",
panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5),
axis.text = element_blank())+
ggthemes::geom_rangeframe(colour = par("col"))
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- destiny::plot(dpt, dcs = dcs, paths_to = TIPs) +
labs(title = panel.text, color = color.lab) +
xlab(labs[1]) +
ylab(labs[2]) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
theme(panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5))
}
print(g)
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
points3D(x = (sign_dim[1]*dms[, dim[1]]),
y = (sign_dim[2]*dms[, dim[2]]),
z = (sign_dim[3]*dms[, dim[3]]),
colvar = color.idx,
col = colimage,
colkey = list(length = 0.3),
phi = phi, theta = theta,
xlab = labs[1],
ylab = labs[2],
zlab = labs[3],
clab = color.lab,
pch = 20,
main = panel.text,
bty = bty,
...)
points3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
col = point.col,
pch = 2,
cex = 1.5,
plot = TRUE,
add = TRUE)
points3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
col = point.col,
pch = 5,
cex = 1.5,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
labels = rep(" Predicted\n Terminal\n Cell",
length(term.idx)),
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
labels = " Root Cell",
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
}
dev.off()
}else{
if (DIMS == 2) {
if (color_by == "SR") {
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- ggplot(dms, aes((sign_dim[1]*dms[, dim[1]]), (sign_dim[2]*dms[, dim[2]]), color = color.idx)) +
geom_point() +
xlab(labs[1]) +
ylab(labs[2]) +
labs(title = panel.text, color = color.lab) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
annotate("point", x = (sign_dim[1]*dms[terminel.idx, dim[1]]),
y = (sign_dim[2]*dms[terminel.idx, dim[2]]),
pch = 20, colour = "red", size = rel(3)) +
scale_color_gradientn(colors = c("lightblue", "skyblue", "darkblue")) +
theme_minimal() +
theme(legend.position = "right",
panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5),
axis.text = element_blank())+
ggthemes::geom_rangeframe(colour = par("col"))
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
g <- destiny::plot(dpt, dcs = dcs, paths_to = TIPs) +
labs(title = panel.text, color = color.lab) +
xlab(labs[1]) +
ylab(labs[2]) +
annotate("text", x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]) - (0.03 * range_y),
label = "Root Cell",
fontface = "bold", colour = "red", size = font.size) +
annotate("text", x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]) + (0.07 * range_y),
label = "Predicted \nTerminal \nCell ",
fontface = "bold", colour = "red", size = font.size) +
theme(panel.grid = element_blank(),
plot.title = element_text(hjust = 0.5))
}
print(g)
}else{
range_y <- max(dms[, dim[2]]) - min(dms[, dim[2]])
points3D(x = (sign_dim[1]*dms[, dim[1]]),
y = (sign_dim[2]*dms[, dim[2]]),
z = (sign_dim[3]*dms[, dim[3]]),
colvar = color.idx,
col = colimage,
colkey = list(length = 0.3),
phi = phi, theta = theta,
xlab = labs[1],
ylab = labs[2],
zlab = labs[3],
clab = color.lab,
pch = 20,
main = panel.text,
bty = bty,
...)
points3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
col = point.col,
pch = 2,
cex = 1.5,
plot = TRUE,
add = TRUE)
points3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
col = point.col,
pch = 5,
cex = 1.5,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[term.idx, dim[1]]),
y = (sign_dim[2]*dms[term.idx, dim[2]]),
z = (sign_dim[3]*dms[term.idx, dim[3]]),
labels = rep(" Predicted\n Terminal\n Cell",
length(term.idx)),
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
text3D(x = (sign_dim[1]*dms[root.idx, dim[1]]),
y = (sign_dim[2]*dms[root.idx, dim[2]]),
z = (sign_dim[3]*dms[root.idx, dim[3]]),
labels = " Root Cell",
col = point.col,
cex = 0.8,
font = 2,
plot = TRUE,
add = TRUE)
}
}
}
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