ggpuar包，绘制CNS级美图

ggpubr 是基于ggplot2 开发出来的包，目的是为了简化ggplot2的操作，便于画出满足论文出版要求的图。网上对于ggpubr包的态度褒贬不一，我们也抱着学习的态度，舔皮论骨是不行的，需要以自己的认知来决定事物的好坏。

一、安装包

install.packages("ggpubr")

二、加载包

library(ggpubr)

三、载入数据

set.seed(1234)
wdata = data.frame(
  sex = factor(rep(c("F", "M"), each=200)),
  weight = c(rnorm(200, 55), rnorm(200, 58)))
  head(wdata, 4)

四、绘图

ggpubr是封装好以ggplot编写的代码，进行简化，就好比Linux 中的alias命令，虽然改变了语法，但是对于不需要学习ggplot2的人，还是比较友好的。

ggdensity(wdata, x = "weight",
          add = "mean", rug = TRUE,
          color = "sex", fill = "sex",
          palette = c("#00AFBB", "#E7B800"))

图片

直方图绘图

gghistogram(wdata, x = "weight",
            add = "mean", rug = TRUE,
            color = "sex", fill = "sex",
            palette = c("#00AFBB", "#E7B800"))

图片

箱线图绘图

data("ToothGrowth")
df <- ToothGrowth
head(df, 4)
p <- ggboxplot(df, x = "dose", y = "len",
               color = "dose", palette =c("#00AFBB", "#E7B800", "#FC4E07"),
               add = "jitter", shape = "dose")
my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
p + stat_compare_means(comparisons = my_comparisons)+ # Add pairwise comparisons p-value
  stat_compare_means(label.y = 50)

图片

小提琴图绘图

ggviolin(df, x = "dose", y = "len", fill = "dose",
         palette = c("#00AFBB", "#E7B800", "#FC4E07"),
         add = "boxplot", add.params = list(fill = "white"))+
  stat_compare_means(comparisons = my_comparisons, label = "p.signif")+ # Add significance levels
  stat_compare_means(label.y = 50)

图片

直方图绘图

data("mtcars")
dfm <- mtcars
# Convert the cyl variable to a factor
dfm$cyl <- as.factor(dfm$cyl)
# Add the name colums
dfm$name <- rownames(dfm)
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg",
          fill = "cyl",               # change fill color by cyl
          color = "white",            # Set bar border colors to white
          palette = "jco",            # jco journal color palett. see ?ggpar
          sort.val = "desc",          # Sort the value in dscending order
          sort.by.groups = FALSE,     # Don't sort inside each group
          x.text.angle = 90           # Rotate vertically x axis texts
)

图片

直方图2

ggbarplot(dfm, x = "name", y = "mpg",
          fill = "cyl",               # change fill color by cyl
          color = "white",            # Set bar border colors to white
          palette = "jco",            # jco journal color palett. see ?ggpar
          sort.val = "asc",           # Sort the value in dscending order
          sort.by.groups = TRUE,      # Sort inside each group
          x.text.angle = 90           # Rotate vertically x axis texts
)

图片

Z-Score绘图

dfm$mpg_z <- (dfm$mpg -mean(dfm$mpg))/sd(dfm$mpg)
dfm$mpg_grp <- factor(ifelse(dfm$mpg_z < 0, "low", "high"),
                      levels = c("low", "high"))
# Inspect the data
head(dfm[, c("name", "wt", "mpg", "mpg_z", "mpg_grp", "cyl")])
ggbarplot(dfm, x = "name", y = "mpg_z",
          fill = "mpg_grp",           # change fill color by mpg_level
          color = "white",            # Set bar border colors to white
          palette = "jco",            # jco journal color palett. see ?ggpar
          sort.val = "asc",           # Sort the value in ascending order
          sort.by.groups = FALSE,     # Don't sort inside each group
          x.text.angle = 90,          # Rotate vertically x axis texts
          ylab = "MPG z-score",
          xlab = FALSE,
          legend.title = "MPG Group"
)

图片

棒棒糖图绘图

ggdotchart(dfm, x = "name", y = "mpg",

图片

Z-Score版棒棒糖绘图

ggdotchart(dfm, x = "name", y = "mpg",
           color = "cyl",                                # Color by groups
           palette = c("#00AFBB", "#E7B800", "#FC4E07"), # Custom color palette
           sorting = "descending",                       # Sort value in descending order
           add = "segments",                             # Add segments from y = 0 to dots
           rotate = TRUE,                                # Rotate vertically
           group = "cyl",                                # Order by groups
           dot.size = 6,                                 # Large dot size
           label = round(dfm$mpg),                        # Add mpg values as dot labels
           font.label = list(color = "white", size = 9,
                             vjust = 0.5),               # Adjust label parameters
         ggtheme = theme_pubr()                        # ggplot2 theme
)

图片

综合以上简单绘图，单从图片质量上可以看出还是比较适用新手操作的，复杂操作据说代码会比较混乱，编写的代码和ggplot原生代码不一样，所以作图的话还是推荐ggplot2。