Question

我想绘制enterotype plot中research所熟悉的图表。但是我的新的multi-ggproto看起来很糟糕，如p1中所示，因为标签的背板颜色缺失。我尝试了多种变体，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labelGrob()和ggplot2包中删除的grid函数。因此，修改的解决方案不起作用。如何在multiple-ggproto中修改标签的背景组颜色。有任何想法吗？提前致谢。这是我的代码和两张图片。 p1：标签的背景颜色应为白色或文字颜色应为黑色。 P2：显示错误的点颜色，线条颜色和图例。

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()

Answer 1

您可以手动更改色阶，使其更加强调背景填充色：

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

您还可以通过更改Alpha值或指定不同的颜色值来调整填充颜色，以便与标签形成更好的对比度。

 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

最后，如果要为标签添加背景白色，则必须删除填充选项。您还可以另外指定形状值。

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（形状边框颜色）相关联。

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如何使用ggplot2修改multiple-ggproto中标签的背景组颜色

1 个答案: