r - ggplot2 每个美学的多个尺度/图例，重新审视

Question

我有一个例子，我想使用 ggplot 突出显示序列比对的几个属性。我正在使用 geom_tile 并希望为两个分数属性设置两组不同颜色的瓷砖。我只能想象一个。

我知道每种美学只有一个比例（以及它背后的逻辑），但也许有人知道如何在这样的情况下破解它，在一个“情节”中使用不同的颜色比例是有意义的。

也许手动添加 Grobs，但我不知道从哪里开始......

另一个问题：由于某种原因override.aes=list(shape = "A")不起作用，有什么想法吗？

再一个：有什么方法可以根据图块的大小（或相反）按比例缩放文本？

library(ggplot2)
library(grid)

pd = data.frame(
  letters = strsplit("AGTGACCGACTATCATAGTGACCCAGAATCATAGTGACCGAGTATGAT", "")[[1]],
  species = rep(c("Human", "Armadillo", "Porcupine"), each=16),
  x       = rep(1:16, 3),
  change  = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
              0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,
              0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0),
  score1  = c(0,0,0,0,0,0,1,1,2,2,2,3,3,3,4,3,
              0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,
              0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
  score2  = c(0,0,0,0,1,1,1,1,0,0,0,0,0,0,0,0,
              0,0,0,0,2,2,2,2,0,0,0,0,0,0,0,0,
              0,0,0,0,3,3,3,3,0,0,0,0,0,0,0,0)
)


ggplot(pd[pd$score1 != 0,], aes(x=x, y=species)) +
  coord_fixed(ratio = 1.5, xlim=c(0.5,16.5), ylim=c(0.5, 3.5)) +
  geom_tile(aes(fill=score1)) +
  scale_fill_gradient2("Score 1", limits=c(0,4),low="#762A83", mid="white", high="#1B7837", guide=guide_colorbar(title.position="top")) +
  geom_text(data=pd, aes(label=letters, color=factor(change)), size=rel(5), family="mono") +
  scale_color_manual("Change", values=c("black", "#F2A11F"), labels=c("None", "Some"), guide=guide_legend(direction="vertical", title.position="top", override.aes=list(shape = "A"))) +
  theme(panel.background=element_rect(fill="white", colour="white"),
        axis.title = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_text(family="mono", size=rel(2)),
        axis.text.x = element_text(size=rel(0.7)),
        legend.text = element_text(size=rel(0.7)),
        legend.key.size = unit(0.7, "lines"),
        legend.position = "bottom", legend.box = "horizontal") +
  ggtitle("What about Score2?")

如何添加另一层不同色阶的瓷砖？

score 9 · Accepted Answer

通过组合来自两个单独生成的地块的 grobs，我设法获得了令人满意的结果。我确信该解决方案可以更好地推广以适应不同的 grob 指数......

library(ggplot2)
library(grid)

pd = data.frame(
  letters = strsplit("AGTGACCGACTATCATAGTGACCCAGAATCATAGTGACCGAGTATGAT", "")[[1]],
  species = rep(c("Human", "Armadillo", "Porcupine"), each=16),
  x       = rep(1:16, 3),
  change  = c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
              0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,
              0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0),
  score1  = c(0,0,0,0,0,0,1,1,2,2,2,3,3,3,4,3,
              0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,
              0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
  score2  = c(0,0,0,0,1,1,1,1,0,0,0,0,0,0,0,0,
              0,0,0,0,2,2,2,2,0,0,0,0,0,0,0,0,
              0,0,0,0,3,3,3,3,0,0,0,0,0,0,0,0)
)


p1=ggplot(pd[pd$score1 != 0,], aes(x=x, y=species)) +
  coord_fixed(ratio = 1.5, xlim=c(0.5,16.5), ylim=c(0.5, 3.5)) +
  geom_tile(aes(fill=score1)) +
  scale_fill_gradient2("Score 1", limits=c(0,4),low="#762A83", mid="white", high="#1B7837", guide=guide_colorbar(title.position="top")) +
  geom_text(data=pd, aes(label=letters, color=factor(change)), size=rel(5), family="mono") +
  scale_color_manual("Change", values=c("black", "#F2A11F"), labels=c("None", "Some"), guide=guide_legend(direction="vertical", title.position="top", override.aes=list(shape = "A"))) +
  theme(panel.background=element_rect(fill="white", colour="white"),
        axis.title = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_text(family="mono", size=rel(2)),
        axis.text.x = element_text(size=rel(0.7)),
        legend.text = element_text(size=rel(0.7)),
        legend.key.size = unit(0.7, "lines"),
        legend.position = "bottom", legend.box = "horizontal") +
  ggtitle("Voila, the Score2!")

p2=ggplot(pd[pd$score2 != 0,], aes(x=x, y=species)) +
  coord_fixed(ratio = 1.5, xlim=c(0.5,16.5), ylim=c(0.5, 3.5)) +
  geom_tile(aes(fill=score2)) +
  scale_fill_gradient2("Score 2", limits=c(0,3),low="#1B7837", mid="white", high="#762A83", guide=guide_colorbar(title.position="top")) +
  geom_text(data=pd, aes(label=letters, color=factor(change)), size=rel(5), family="mono") +
  scale_color_manual("Change", values=c("black", "#F2A11F"), labels=c("None", "Some"), guide=guide_legend(direction="vertical", title.position="top", override.aes=list(shape = "A"))) +
  theme(panel.background=element_rect(fill="white", colour="white"),
        axis.title = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_text(family="mono", size=rel(2)),
        axis.text.x = element_text(size=rel(0.7)),
        legend.text = element_text(size=rel(0.7)),
        legend.key.size = unit(0.7, "lines"),
        legend.position = "bottom", legend.box = "horizontal") +
  ggtitle("What about Score2?")


p1g=ggplotGrob(p1)
p2g=ggplotGrob(p2)

combo.grob = p1g

combo.grob$grobs[[8]] = cbind(p1g$grobs[[8]][,1:4], 
                              p2g$grobs[[8]][,3:5], 
                              size="first")

combo.grob$grobs[[4]] = reorderGrob(
                          addGrob(p1g$grobs[[4]], 
                                  getGrob(p2g$grobs[[4]], 
                                          "geom_rect.rect", 
                                          grep=TRUE)), 
                          c(1,2,5,3,4))
grid.newpage()
grid.draw(combo.grob)

一个地块中的两个尺度

score 5 · Accepted Answer

我会使用文本大小来表示 score2：

ggplot(pd[pd$score1 != 0,], aes(x=x, y=species)) +
  coord_fixed(ratio = 1.5, xlim=c(0.5,16.5), ylim=c(0.5, 3.5)) +
  geom_tile(aes(fill=score1)) +
  scale_fill_gradient2("Score 1", limits=c(0,4),low="#762A83", mid="white", high="#1B7837", guide=guide_colorbar(title.position="top")) +
  geom_text(data=pd, aes(label=letters, size = score2, color=factor(change)), family="mono") +
  scale_size_continuous(range = c(4, 8)) +
  scale_color_manual("Change", values=c("black", "#F2A11F"), labels=c("None", "Some"), guide=guide_legend(direction="vertical", title.position="top", override.aes=list(shape = "A"))) +
  theme(panel.background=element_rect(fill="white", colour="white"),
        axis.title = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_text(family="mono", size=rel(2)),
        axis.text.x = element_text(size=rel(0.7)),
        legend.text = element_text(size=rel(0.7)),
        legend.key.size = unit(0.7, "lines"),
        legend.position = "bottom", legend.box = "horizontal") +
  ggtitle("What about Score2?")

在此处输入图像描述

更新：

这是一个快速的技巧，我不确定这是否容易目视检查......

library(ggplot2)
library(grid)
library(proto)

GeomTile2 <- proto(ggplot2:::GeomTile, {
  reparameterise <- function(., df, params) {
    df <- .$.super$reparameterise(df, params)
    if (params$ud == "u") 
      transform(df, ymin = y) 
    else 
        transform(df, ymax = (y-ymin)*0.8 + ymin, ymin = (y-ymin)*0.2 + ymin)
  }
  draw <- function(..., ud) {.$.super$draw(..., ud)}
})
geom_tile2 <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ..., ud = "u") { 
  GeomTile2$new(mapping = mapping, data = data, stat = stat, position = position, ..., ud = ud)
}

ggplot(pd, aes(x=x, y=species)) +
  coord_fixed(ratio = 1.5, xlim=c(0.5,16.5), ylim=c(0.5, 3.5)) +
  geom_tile2(aes(fill=score1), ud = "u") +
  geom_tile2(aes(fill = score2), ud = "d") +
  scale_fill_gradient2("Score 1", limits=c(0,4),low="#762A83", mid="white", high="#1B7837", guide=guide_colorbar(title.position="top")) +
  geom_text(data=pd, aes(label=letters, color=factor(change)), size=rel(5), family="mono") +
  scale_color_manual("Change", values=c("black", "#F2A11F"), labels=c("None", "Some"), guide=guide_legend(direction="vertical", title.position="top", override.aes=list(shape = "A"))) +
  theme(panel.background=element_rect(fill="white", colour="white"),
        axis.title = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text.y = element_text(family="mono", size=rel(2)),
        axis.text.x = element_text(size=rel(0.7)),
        legend.text = element_text(size=rel(0.7)),
        legend.key.size = unit(0.7, "lines"),
        legend.position = "bottom", legend.box = "horizontal") +
  ggtitle("What about Score2?")

在此处输入图像描述

上半部分表示 score1，下半部分表示 score2。

r - ggplot2 每个美学的多个尺度/图例，重新审视

2 回答 2

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