如何使用ggplot2修改多ggproto中标签的背景颜色
How to modify the backgroup color of label in the multiple-ggproto using ggplot2
我想画一个enterotype plot in the research熟悉的图形。但是我的新 multiple-ggproto 看起来很糟糕，如 p1 所示，因为缺少标签的背景颜色。我已经尝试了多种变体，例如修改 GeomLabel$draw_panel 以重置 ggplot2::ggproto 中 geom 的默认参数。但是，我找不到在 ggplot2 和 grid 包中删除的 labelGrob() 函数。因此，修改的解决方案不起作用。如何在 multiple-ggproto.xml 中修改 label 的 backgroup 颜色。有任何想法吗？提前致谢。这是我的代码和两张图片。
p1: label 的底色为白色或文字颜色为黑色。
P2：显示错误的点颜色、线颜色和图例。
geom_enterotype <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity",
alpha = 0.3, prop = 0.5, ..., lineend = "butt", linejoin = "round",
linemitre = 1, arrow = NULL, na.rm = FALSE, parse = FALSE,
nudge_x = 0, nudge_y = 0, label.padding = unit(0.15, "lines"),
label.r = unit(0.15, "lines"), label.size = 0.1,
show.legend = TRUE, inherit.aes = TRUE) {
library(ggplot2)
# create new stat and geom for PCA scatterplot with ellipses
StatEllipse <- ggproto("StatEllipse", Stat,
required_aes = c("x", "y"),
compute_group = function(., data, scales, level = 0.75, segments = 51, ...) {
library(MASS)
dfn <- 2
dfd <- length(data$x) - 1
if (dfd < 3) {
ellipse <- rbind(c(NA, NA))
} else {
v <- cov.trob(cbind(data$x, data$y))
shape <- v$cov
center <- v$center
radius <- sqrt(dfn * qf(level, dfn, dfd))
angles <- (0:segments) * 2 * pi/segments
unit.circle <- cbind(cos(angles), sin(angles))
ellipse <- t(center + radius * t(unit.circle %*% chol(shape)))
}
ellipse <- as.data.frame(ellipse)
colnames(ellipse) <- c("x", "y")
return(ellipse)
})
# write new ggproto
GeomEllipse <- ggproto("GeomEllipse", Geom,
draw_group = function(data, panel_scales, coord) {
n <- nrow(data)
if (n == 1)
return(zeroGrob())
munched <- coord_munch(coord, data, panel_scales)
munched <- munched[order(munched$group), ]
first_idx <- !duplicated(munched$group)
first_rows <- munched[first_idx, ]
grid::pathGrob(munched$x, munched$y, default.units = "native",
id = munched$group,
gp = grid::gpar(col = first_rows$colour,
fill = alpha(first_rows$fill, first_rows$alpha), lwd = first_rows$size * .pt, lty = first_rows$linetype))
},
default_aes = aes(colour = "NA", fill = "grey20", size = 0.5, linetype = 1, alpha = NA, prop = 0.5),
handle_na = function(data, params) {
data
},
required_aes = c("x", "y"),
draw_key = draw_key_path
)
# create a new stat for PCA scatterplot with lines which totally directs to the center
StatConline <- ggproto("StatConline", Stat,
compute_group = function(data, scales) {
library(miscTools)
library(MASS)
df <- data.frame(data$x,data$y)
mat <- as.matrix(df)
center <- cov.trob(df)$center
names(center)<- NULL
mat_insert <- insertRow(mat, 2, center )
for(i in 1:nrow(mat)) {
mat_insert <- insertRow( mat_insert, 2*i, center )
next
}
mat_insert <- mat_insert[-c(2:3),]
rownames(mat_insert) <- NULL
mat_insert <- as.data.frame(mat_insert,center)
colnames(mat_insert) =c("x","y")
return(mat_insert)
},
required_aes = c("x", "y")
)
# create a new stat for PCA scatterplot with center labels
StatLabel <- ggproto("StatLabel" ,Stat,
compute_group = function(data, scales) {
library(MASS)
df <- data.frame(data$x,data$y)
center <- cov.trob(df)$center
names(center)<- NULL
center <- t(as.data.frame(center))
center <- as.data.frame(cbind(center))
colnames(center) <- c("x","y")
rownames(center) <- NULL
return(center)
},
required_aes = c("x", "y")
)
layer1 <- layer(data = data, mapping = mapping, stat = stat, geom = GeomPoint,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(na.rm = na.rm, ...))
layer2 <- layer(stat = StatEllipse, data = data, mapping = mapping, geom = GeomEllipse, position = position, show.legend = FALSE,
inherit.aes = inherit.aes, params = list(na.rm = na.rm, prop = prop, alpha = alpha, ...))
layer3 <- layer(data = data, mapping = mapping, stat = StatConline, geom = GeomPath,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(lineend = lineend, linejoin = linejoin,
linemitre = linemitre, arrow = arrow, na.rm = na.rm, ...))
if (!missing(nudge_x) || !missing(nudge_y)) {
if (!missing(position)) {
stop("Specify either `position` or `nudge_x`/`nudge_y`",
call. = FALSE)
}
position <- position_nudge(nudge_x, nudge_y)
}
layer4 <- layer(data = data, mapping = mapping, stat = StatLabel, geom = GeomLabel,
position = position, show.legend = FALSE, inherit.aes = inherit.aes,
params = list(parse = parse, label.padding = label.padding,
label.r = label.r, label.size = label.size, na.rm = na.rm, ...))
return(list(layer1,layer2,layer3,layer4))
}
# data
data(Cars93, package = "MASS")
car_df <- Cars93[, c(3, 5, 13:15, 17, 19:25)]
car_df <- subset(car_df, Type == "Large" | Type == "Midsize" | Type == "Small")
x1 <- mean(car_df$Price) + 2 * sd(car_df$Price)
x2 <- mean(car_df$Price) - 2 * sd(car_df$Price)
car_df <- subset(car_df, Price > x2 | Price < x1)
car_df <- na.omit(car_df)
# Principal Component Analysis
car.pca <- prcomp(car_df[, -1], scale = T)
car.pca_pre <- cbind(as.data.frame(predict(car.pca)[, 1:2]), car_df[, 1])
colnames(car.pca_pre) <- c("PC1", "PC2", "Type")
xlab <- paste("PC1(", round(((car.pca$sdev[1])^2/sum((car.pca$sdev)^2)), 2) * 100, "%)", sep = "")
ylab <- paste("PC2(", round(((car.pca$sdev[2])^2/sum((car.pca$sdev)^2)), 2) * 100, "%)", sep = "")
head(car.pca_pre)
#plot
library(ggplot2)
p1 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , color= Type ,label = Type)) +
geom_enterotype()
p2 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , label = Type)) +
geom_enterotype()
您可以手动更改色阶，使其比背景填充颜色更加突出：
p3 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , color = Type, label = Type)) +
geom_enterotype() +
scale_colour_manual(values = c("red4", "green4", "blue4"))
p3
您还可以通过更改 alpha 值或分配不同的颜色值来调整填充颜色，以提供更好的标签对比度。
p4 <- ggplot(car.pca_pre, aes(PC1, PC2, label = Type, shape = Type, fill = Type, colour = Type)) +
geom_enterotype() +
scale_fill_manual(values = alpha(c("pink", "lightgreen", "skyblue"), 1)) +
scale_colour_manual(values = c("red4", "green4", "blue4"))
p4
最后，如果您希望标签的背景颜色为白色，则必须删除填充选项。您还可以另外指定一个形状值。
如您所见，背景文本颜色与形状填充颜色相关联，而文本标签颜色与线条颜色相关联，即形状边框颜色。
p5 <- ggplot(car.pca_pre, aes(PC1, PC2, label = Type, shape = Type, colour = Type)) +
geom_enterotype() + scale_colour_manual(values = c("red4", "green4", "blue4"))
p5
我想画一个enterotype plot in the research熟悉的图形。但是我的新 multiple-ggproto 看起来很糟糕，如 p1 所示，因为缺少标签的背景颜色。我已经尝试了多种变体，例如修改 GeomLabel$draw_panel 以重置 ggplot2::ggproto 中 geom 的默认参数。但是，我找不到在 ggplot2 和 grid 包中删除的 labelGrob() 函数。因此，修改的解决方案不起作用。如何在 multiple-ggproto.xml 中修改 label 的 backgroup 颜色。有任何想法吗？提前致谢。这是我的代码和两张图片。
p1: label 的底色为白色或文字颜色为黑色。
P2：显示错误的点颜色、线颜色和图例。
geom_enterotype <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity",
alpha = 0.3, prop = 0.5, ..., lineend = "butt", linejoin = "round",
linemitre = 1, arrow = NULL, na.rm = FALSE, parse = FALSE,
nudge_x = 0, nudge_y = 0, label.padding = unit(0.15, "lines"),
label.r = unit(0.15, "lines"), label.size = 0.1,
show.legend = TRUE, inherit.aes = TRUE) {
library(ggplot2)
# create new stat and geom for PCA scatterplot with ellipses
StatEllipse <- ggproto("StatEllipse", Stat,
required_aes = c("x", "y"),
compute_group = function(., data, scales, level = 0.75, segments = 51, ...) {
library(MASS)
dfn <- 2
dfd <- length(data$x) - 1
if (dfd < 3) {
ellipse <- rbind(c(NA, NA))
} else {
v <- cov.trob(cbind(data$x, data$y))
shape <- v$cov
center <- v$center
radius <- sqrt(dfn * qf(level, dfn, dfd))
angles <- (0:segments) * 2 * pi/segments
unit.circle <- cbind(cos(angles), sin(angles))
ellipse <- t(center + radius * t(unit.circle %*% chol(shape)))
}
ellipse <- as.data.frame(ellipse)
colnames(ellipse) <- c("x", "y")
return(ellipse)
})
# write new ggproto
GeomEllipse <- ggproto("GeomEllipse", Geom,
draw_group = function(data, panel_scales, coord) {
n <- nrow(data)
if (n == 1)
return(zeroGrob())
munched <- coord_munch(coord, data, panel_scales)
munched <- munched[order(munched$group), ]
first_idx <- !duplicated(munched$group)
first_rows <- munched[first_idx, ]
grid::pathGrob(munched$x, munched$y, default.units = "native",
id = munched$group,
gp = grid::gpar(col = first_rows$colour,
fill = alpha(first_rows$fill, first_rows$alpha), lwd = first_rows$size * .pt, lty = first_rows$linetype))
},
default_aes = aes(colour = "NA", fill = "grey20", size = 0.5, linetype = 1, alpha = NA, prop = 0.5),
handle_na = function(data, params) {
data
},
required_aes = c("x", "y"),
draw_key = draw_key_path
)
# create a new stat for PCA scatterplot with lines which totally directs to the center
StatConline <- ggproto("StatConline", Stat,
compute_group = function(data, scales) {
library(miscTools)
library(MASS)
df <- data.frame(data$x,data$y)
mat <- as.matrix(df)
center <- cov.trob(df)$center
names(center)<- NULL
mat_insert <- insertRow(mat, 2, center )
for(i in 1:nrow(mat)) {
mat_insert <- insertRow( mat_insert, 2*i, center )
next
}
mat_insert <- mat_insert[-c(2:3),]
rownames(mat_insert) <- NULL
mat_insert <- as.data.frame(mat_insert,center)
colnames(mat_insert) =c("x","y")
return(mat_insert)
},
required_aes = c("x", "y")
)
# create a new stat for PCA scatterplot with center labels
StatLabel <- ggproto("StatLabel" ,Stat,
compute_group = function(data, scales) {
library(MASS)
df <- data.frame(data$x,data$y)
center <- cov.trob(df)$center
names(center)<- NULL
center <- t(as.data.frame(center))
center <- as.data.frame(cbind(center))
colnames(center) <- c("x","y")
rownames(center) <- NULL
return(center)
},
required_aes = c("x", "y")
)
layer1 <- layer(data = data, mapping = mapping, stat = stat, geom = GeomPoint,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(na.rm = na.rm, ...))
layer2 <- layer(stat = StatEllipse, data = data, mapping = mapping, geom = GeomEllipse, position = position, show.legend = FALSE,
inherit.aes = inherit.aes, params = list(na.rm = na.rm, prop = prop, alpha = alpha, ...))
layer3 <- layer(data = data, mapping = mapping, stat = StatConline, geom = GeomPath,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(lineend = lineend, linejoin = linejoin,
linemitre = linemitre, arrow = arrow, na.rm = na.rm, ...))
if (!missing(nudge_x) || !missing(nudge_y)) {
if (!missing(position)) {
stop("Specify either `position` or `nudge_x`/`nudge_y`",
call. = FALSE)
}
position <- position_nudge(nudge_x, nudge_y)
}
layer4 <- layer(data = data, mapping = mapping, stat = StatLabel, geom = GeomLabel,
position = position, show.legend = FALSE, inherit.aes = inherit.aes,
params = list(parse = parse, label.padding = label.padding,
label.r = label.r, label.size = label.size, na.rm = na.rm, ...))
return(list(layer1,layer2,layer3,layer4))
}
# data
data(Cars93, package = "MASS")
car_df <- Cars93[, c(3, 5, 13:15, 17, 19:25)]
car_df <- subset(car_df, Type == "Large" | Type == "Midsize" | Type == "Small")
x1 <- mean(car_df$Price) + 2 * sd(car_df$Price)
x2 <- mean(car_df$Price) - 2 * sd(car_df$Price)
car_df <- subset(car_df, Price > x2 | Price < x1)
car_df <- na.omit(car_df)
# Principal Component Analysis
car.pca <- prcomp(car_df[, -1], scale = T)
car.pca_pre <- cbind(as.data.frame(predict(car.pca)[, 1:2]), car_df[, 1])
colnames(car.pca_pre) <- c("PC1", "PC2", "Type")
xlab <- paste("PC1(", round(((car.pca$sdev[1])^2/sum((car.pca$sdev)^2)), 2) * 100, "%)", sep = "")
ylab <- paste("PC2(", round(((car.pca$sdev[2])^2/sum((car.pca$sdev)^2)), 2) * 100, "%)", sep = "")
head(car.pca_pre)
#plot
library(ggplot2)
p1 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , color= Type ,label = Type)) +
geom_enterotype()
p2 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , label = Type)) +
geom_enterotype()
您可以手动更改色阶，使其比背景填充颜色更加突出：
p3 <- ggplot(car.pca_pre, aes(PC1, PC2, fill = Type , color = Type, label = Type)) +
geom_enterotype() +
scale_colour_manual(values = c("red4", "green4", "blue4"))
p3
p4 <- ggplot(car.pca_pre, aes(PC1, PC2, label = Type, shape = Type, fill = Type, colour = Type)) +
geom_enterotype() +
scale_fill_manual(values = alpha(c("pink", "lightgreen", "skyblue"), 1)) +
scale_colour_manual(values = c("red4", "green4", "blue4"))
p4
最后，如果您希望标签的背景颜色为白色，则必须删除填充选项。您还可以另外指定一个形状值。
如您所见，背景文本颜色与形状填充颜色相关联，而文本标签颜色与线条颜色相关联，即形状边框颜色。
p5 <- ggplot(car.pca_pre, aes(PC1, PC2, label = Type, shape = Type, colour = Type)) +
geom_enterotype() + scale_colour_manual(values = c("red4", "green4", "blue4"))
p5