R語言可視化學習筆記之ggridges包

作者：嚴濤 浙江大學作物遺傳育種在讀研究生（生物信息學方向）偽碼農，R語言愛好者，愛開源。

簡介

ggridges包主要用來繪製山巒圖。尤其是針對時間或者空間分布可視化具有十分好的效果。ggridges主要提供兩個幾何圖像函數：

具體用法可以參考官方文檔：

https://cran.r-project.org/web/packages/ggridges/vignettes/introduction.html

geom_ridgeline()

library(ggridges)
library(tidyverse)
# grid.arrange來自於gridExtra包，可以同時拼圖多個ggplot2對象
library(gridExtra)


my_data <- data.frame(x=1:5, y=rep(1,5), height=c(0,1,-1,3,2))
plot_base <- ggplot(my_data, aes(x, y, height=height))

# 默認負值不顯示，除非指定min_height參數

grid.arrange(plot_base+geom_ridgeline(),
            plot_base+geom_ridgeline(min_height=-2), ncol=2)

geom_density_ridges()

geom_density_ridges()函數首先會根據數據計算密度然後繪圖，此時美學映射height沒有必要寫入函數中。下面使用lincoln_weather數據集。

# creates a vector of n equally spaced colors along the
# Matplolib 'viridis' color map

# also designed to be perceived by readers with the most common form of color blindness
#  scale_fill_viridis函數來源於此包，
# 其參數 option用於設置顏色 "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"),
and "viridis" (or "D", the default option).
# ?viridis可以查看其具體含義

library(viridis)
head(lincoln_weather[ ,1:4])


## # A tibble: 6 x 4
##   CST      `Max Temperature [F]` `Mean Temperature [F]` `Min Temperature ~
##   <chr>                    <int>                  <int>              <int>
## 1 2016-1-1                    37                     24                 11
## 2 2016-1-2                    41                     23                  5
## 3 2016-1-3                    37                     23                  8
## 4 2016-1-4                    30                     17                  4
## 5 2016-1-5                    38                     29                 19
## 6 2016-1-6                    34                     33                 32

# x後的值用 ` (反引號)括起，是因為列名字中存在空格和特殊字符，需要特殊對待
# fill = ..x..， double dots是ggplot2的一種特殊識別符，用來區分定義的和計算的美學參數
# 這裡指用橫軸的數據著色

ggplot(lincoln_weather, aes(x=`Mean Temperature [F]`, y=`Month`, fill=..x..))+
 geom_density_ridges_gradient(scale=3, rel_min_height=0.01, gradient_lwd = 1.)+
 scale_x_continuous(expand = c(0.01, 0))+ # 擴展下橫軸和縱軸
 scale_y_discrete(expand = c(0.01,0))+
 scale_fill_viridis(name="Temp. [F]", option = "C")+
 labs(title="Temperature in Lincoln NE",
      subtitle="Mean temperature (Fahrenheit) by month for 2016\nData:Orogin CSV from the Weather Underground ")+
 theme_ridges(font_size = 13, grid = FALSE)+
 theme(axis.title.y = element_blank())

cyclinal scales

為了使得ggridges繪製的圖形可視化效果最好，同時為了減少用戶對顏色設置的困難，作者提供了cyclinal scales用於顏色輪轉映射。

ggplot(diamonds, aes(x=price, y=cut, fill=cut))+
 geom_density_ridges(scale=4)+
 scale_fill_cyclical(values = c("blue", "green"))+
 theme_ridges(grid = FALSE)

默認的，cyclinal scales為了防止誤解是不繪製圖例的，但是可以通過選項guide="legend"添加圖例。

ggplot(diamonds, aes(x=price, y=cut, fill=cut))+
 geom_density_ridges(scale=4)+
 scale_fill_cyclical(values = c("blue", "green"), guide="legend")+
 theme_ridges(grid = FALSE)

跟ggplot2一樣，圖例是可以修改的,其他參數比如大小、透明度、形狀等都是可以通過cyclinal scales修改。

ggplot(diamonds, aes(x=price, y=cut, fill=cut))+
 geom_density_ridges(scale=4)+
 scale_fill_cyclical(values = c("blue", "green"), guide="legend",
                     labels=c("Fair"="blue", "Good"="green"),
                     name="Fill colors")+
 theme_ridges(grid = FALSE)

再來2個示例

不做解釋了，如果想重現就把代碼拆解開，按需修改。一句句話單獨拆開運行，理解其操作內容。

library(dplyr)
library(forcats)
Catalan_elections %>%
 mutate(YearFct = fct_rev(as.factor(Year))) %>%
 ggplot(aes(y = YearFct)) +
 geom_density_ridges(
   aes(x = Percent, fill = paste(YearFct, Option)),
   alpha = .8, color = "white", from = 0, to = 100
 ) +
 labs(
   x = "Vote (%)",
   y = "Election Year",
   title = "Indy vs Unionist vote in Catalan elections",
   subtitle = "Analysis unit: municipalities (n = 949)",
   caption = "Marc Belzunces (@marcbeldata) | Source: Idescat"
 ) +
 scale_y_discrete(expand = c(0.01, 0)) +
 scale_x_continuous(expand = c(0.01, 0)) +
 scale_fill_cyclical(
   breaks = c("1980 Indy", "1980 Unionist"),
   labels = c(`1980 Indy` = "Indy", `1980 Unionist` = "Unionist"),
   values = c("#ff0000", "#0000ff", "#ff8080", "#8080ff"),
   name = "Option", guide = "legend"
 ) +
 theme_ridges(grid = FALSE)

library(DAAG) # for ais dataset
ais$sport <- factor(
 ais$sport,
 levels = c("B_Ball", "Field", "Gym", "Netball", "Row", "Swim", "T_400m", "T_Sprnt", "Tennis", "W_Polo"),
 labels = c("Basketball", "Field", "Gym", "Netball", "Row", "Swim", "Track 400m", "Track Sprint", "Tennis", "Water Polo")
)

ggplot(ais, aes(x=ht, y=sport, color=sex, point_color=sex, fill=sex)) +
 geom_density_ridges(
   jittered_points=TRUE, scale = .95, rel_min_height = .01,
   point_shape = "|", point_size = 3, size = 0.25,
   position = position_points_jitter(height = 0)
 ) +
 scale_y_discrete(expand = c(.01, 0)) +
 scale_x_continuous(expand = c(0, 0), name = "height [cm]") +
 scale_fill_manual(values = c("#D55E0050", "#0072B250"), labels = c("female", "male")) +
 scale_color_manual(values = c("#D55E00", "#0072B2"), guide = "none") +
 scale_discrete_manual("point_color", values = c("#D55E00", "#0072B2"), guide = "none") +
 guides(fill = guide_legend(
   override.aes = list(
     fill = c("#D55E00A0", "#0072B2A0"),
     color = NA, point_color = NA))
 ) +
 ggtitle("Height in Australian athletes") +
 theme_ridges(center = TRUE)

還有很多用法有興趣的可以查看官方文檔https://cran.r-project.org/web/packages/ggridges/vignettes/introduction.html和https://cran.r-project.org/web/packages/ggridges/vignettes/gallery.html）繼續學習。

嚴濤老師的繪圖教程還有：

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