R语言如何绘制云雨图（20）

1.什么是云雨图？

云雨图，顾名思义，由2部分组成，上方的半个小提琴图形似云朵，下方的点图形似雨滴。

上方的半个小提琴图，类似于核密度曲线，其曲线下的面积是1。

下方的点图，其实是频率分布直方图的点状抽象。

2.绘图前的数据准备

​ demo数据可以在https://www.bioladder.cn/shiny/zyp/bioladder2/demoData/rainCloud/demo.txt下载。

​ 包含2个维度的数据，通常每一列是个样本，每一行是个基因

3. R语言怎么画云雨图

# 加载R包，没有安装请先安装  install.packages("包名") 
library(ggplot2)
library(reshape2)
library(RColorBrewer)
library(grid)# 读取云雨图数据文件
df = read.delim("https://www.bioladder.cn/shiny/zyp/bioladder2/demoData/rainCloud/demo.txt",# 这里读取了网络上的demo数据，将此处换成你自己电脑里的文件header = T       # 指定第一行是列名
)
# 把数据转换成ggplot常用的类型（长数据）
df = melt(df)                    # melt出自reshape2包
head(df)                         # 查看转换完成的数据的前几行
# 绘图
ggplot(df,aes(x=variable,   y=value,fill=variable,     # fill填充颜色，根据变量名赋值colour=variable))+ # colour图形边界颜色，根据变量名赋值geom_flat_violin(position = position_nudge(x=.1))+ # 见下段代码geom_dotplot(binaxis = "y",binwidth = 0.1,   # 雨滴间隙stackdir = "down",dotsize = 0.6)+   # 雨滴大小coord_flip()+                  # 翻转坐标轴theme_classic()                # ggplot2主题

geom_flat_violin函数代码

#<<<<<<<<<<<<<<<<<<<<<<<<
# 由于ggplot2并没有提供半小提琴图，所以经由geom_violin的源码修改成geom_flat_violin函数
"%||%" <- function(a, b) {if (!is.null(a)) a else b
}color<-brewer.pal(7,"Set2")[c(1,2,4,5)]geom_flat_violin <- function(mapping = NULL, data = NULL, stat = "ydensity",position = "dodge", trim = TRUE, scale = "area",show.legend = NA, inherit.aes = TRUE, ...) {layer(data = data,mapping = mapping,stat = stat,geom = GeomFlatViolin,position = position,show.legend = show.legend,inherit.aes = inherit.aes,params = list(trim = trim,scale = scale,...))
}GeomFlatViolin <-ggproto("GeomFlatViolin", Geom,setup_data = function(data, params) {data$width <- data$width %||%params$width %||% (resolution(data$x, FALSE) * 0.9)data %>%group_by(group) %>%mutate(ymin = min(y),ymax = max(y),xmin = x,xmax = x + width / 2)},draw_group = function(data, panel_scales, coord) {data <- transform(data, xminv = x,xmaxv = x + violinwidth * (xmax - x)) newdata <- rbind(plyr::arrange(transform(data, x = xmaxv), -y),plyr::arrange(transform(data, x = xminv), y))newdata_Polygon <- rbind(newdata, newdata[1,])newdata_Polygon$colour<-NAnewdata_Path <- plyr::arrange(transform(data, x = xmaxv), -y)ggplot2:::ggname("geom_flat_violin", grobTree(GeomPolygon$draw_panel(newdata_Polygon, panel_scales, coord),GeomPath$draw_panel(newdata_Path, panel_scales, coord)))},draw_key = draw_key_polygon,default_aes = aes(weight = 1, colour = "grey20", fill = "white", size = 0.5,alpha = NA, linetype = "solid"),required_aes = c("x", "y"))findParams <- function(mu, sigma, skew, kurt) {value <- .C("JohnsonMomentFitR", as.double(mu), as.double(sigma),as.double(skew), as.double(kurt - 3), gamma = double(1),delta = double(1), xi = double(1), lambda = double(1),type = integer(1), PACKAGE = "SuppDists")list(gamma = value$gamma, delta = value$delta,xi = value$xi, lambda = value$lambda,type = c("SN", "SL", "SU", "SB")[value$type])
}
#>>>>>>>>>>>>>>>>>>>>>>>>

4. BioLadder生信云平台在线绘制云雨图

不想写代码？可以用BioLadder生信云平台在线绘制云雨图。

网址：https://www.bioladder.cn/web/#/chart/47