R IN ACTION SELF-TUTORIAL-17 gganatogram 人体解剖、动物器官与细胞包的安装与使用 2020-06-09

**条件：ggplot2 ,ggpolypath
1、首先安装对应的包：

devtools::install_github("jespermaag/gganatogram")
install.packages('shiny')
install.packages('dplyr')
install.packages("viridis")
install.packages("gridExtra")
library(gganatogram)
library(dplyr)
library(viridis)
library(gridExtra)
hgMale <- gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") + theme_void()
hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") + theme_void()
mmMale <- gganatogram(data=mmMale_key, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour") + theme_void()
mmFemale <- gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour")  +theme_void()  
grid.arrange(hgMale, hgFemale, mmMale, mmFemale, ncol=4)
hgMale <- gganatogram(data=hgMale_key, fillOutline='#440154FF', organism='human', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#440154FF', organism='human', sex='female', fill="value") + theme_void() +  scale_fill_viridis()
mmMale <- gganatogram(data=mmMale_key, fillOutline='#440154FF', organism='mouse', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
mmFemale <- gganatogram(data=mmFemale_key, outline = T, fillOutline='#440154FF', organism='mouse', sex='female', fill="value")  +theme_void()   +  scale_fill_viridis()
grid.arrange(hgMale, hgFemale, mmMale, mmFemale, ncol=2)
organPlot <- data.frame(organ = c("heart", "leukocyte", "nerve", "brain", "liver", "stomach", "colon"), 
 type = c("circulation", "circulation",  "nervous system", "nervous system", "digestion", "digestion", "digestion"), 
 colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"), 
 value = c(10, 5, 1, 8, 2, 5, 5), 
 stringsAsFactors=F)

 head(organPlot)
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour")

会得到以下图

image.png

去掉标尺与背景：

gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +  theme_void()

image.png

查看还可以进行注释的器官：

hgMale_key$organ

画出男性：

gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +theme_void()

image.png

去掉外周,只留下神经系统：

organPlot %>%
    dplyr::filter(type %in% c('circulation', 'nervous system')) %>%
gganatogram(outline=F, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") + 
theme_void()

image.png

gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="value") + 
theme_void() +
scale_fill_gradient(low = "white", high = "red")

image.png

画出部分器官：如心脏，肝脏，胃等。

  colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"), 
 value = c(10, 5, 1, 8, 2, 5, 5), 
 type = rep('Normal', 7), 
 stringsAsFactors=F),
 data.frame(organ = c("heart", "leukocyte", "nerve", "brain", "liver", "stomach", "colon"), 
  colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"), 
 value = c(5, 5, 10, 8, 2, 5, 5), 
 type = rep('Cancer', 7), 
 stringsAsFactors=F))

image.png

两组比较图：

gganatogram(data=compareGroups, fillOutline='#a6bddb', organism='human', sex='male', fill="value") + 
theme_void() +
facet_wrap(~type) +
scale_fill_gradient(low = "white", high = "red")

image.png

多个系统的实现：

gganatogram(data=hgMale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
facet_wrap(~type, ncol=4) +
theme_void()

image.png

2、查看女性器官列表：

hgFemale_key$organ

查看空白的女性器官图：

gganatogram(data=hgFemale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour")  +theme_void()

查看女性不同系统图：

gganatogram(data=hgFemale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +
facet_wrap(~type, ncol=4) +
theme_void()

image.png

女性生殖系统的实现：

hgFemale_key %>%
    dplyr::filter(type=='reproductive') %>%
    gganatogram( outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour")  +
    theme_void()  +
coord_cartesian(xlim = c(30, 75), ylim = c(-110, -80))

image.png

3、小鼠器官的实现：

gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour")  +theme_void()  +coord_fixed()

image.png

小鼠主要器官的实现：

gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour")  +theme_void()+facet_wrap(~type, ncol=4)
mmFemale_key$organ

雌鼠主要器官的实现：

gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour")  +theme_void()    +coord_fixed()

image.png

4、细胞的实现：

length(cell_key) 
#> [1] 1
cell_key##查看细胞的大小与类型等

image.png

gganatogram(data=cell_key[['cell']], outline = T, fillOutline='steelblue', organism="cell", fill="colour")  +theme_void()   + coord_fixed()

image.png

5、别的动物与器官：

length(other_key)
#> [1] 24
names(other_key)

image.png

library(gridExtra)
plotList <- list()
for (organism in names(other_key)) {
    plotList[[organism]] <- gganatogram(data=other_key[[organism]], outline = T, fillOutline='white', organism=organism, sex='female', fill="colour")  +
                theme_void() +
                ggtitle(organism) + 
                theme(plot.title = element_text(hjust=0.5, size=9)) + 
                coord_fixed()
}
do.call(grid.arrange,  c(plotList[1:4], ncol=2))

image.png