我有物种和不同样本的数量，这些物种属于一个特定的群体。
我想展示的是一个情节，其中不同的物种按其群体着色。所以每个物种都有自己的颜色，但根据它们所属的群体有不同的色调。例如。所有细菌呈灰色阴影，所有树木呈绿色阴影，所有藻类呈蓝色阴影。
理想情况下，图例也将按这些组进行分组。
这是我的数据的结构方式:
library("ggplot2")
library("tidyverse")
mydata <- data.frame(counts=c(560, 310, 250, 243, 124, 306, 1271, 112, 201, 305, 201, 304, 136, 211, 131 ),
species=c("bact1", "bact1", "shrub1", "shrub1", "tree1", "tree1", "tree2", "algae1", "algae1", "bact2", "bact3", "tree3", "algae2", "shrub2", "shrub2"),
sample=c(1,2,1,1,2,2,1,1,2,2,2,2,1,1,2),
group=c("bacterium", "bacterium", "shrub", "shrub", "tree", "tree", "tree", "algae", "algae", "bacterium", "bacterium", "tree", "algae", "shrub", "shrub"))
> mydata
# A tibble: 15 x 4
counts species sample group
<dbl> <chr> <dbl> <fct>
1 560 bact1 1 bacterium
2 310 bact1 2 bacterium
3 250 a-tree1 1 tree
4 243 c-tree2 1 tree
5 124 c-tree1 2 tree
6 306 a-tree1 2 tree
7 1271 tree2 1 tree
8 112 algae1 1 algae
9 201 algae1 2 algae
10 305 bact2 2 bacterium
11 201 bact3 2 bacterium
12 304 tree3 2 tree
13 136 algae2 1 algae
14 211 tree2 1 tree
15 131 tree2 2 tree
我已经得到了漂亮的堆叠条形图，但是颜色只是按照标签的顺序给出，按字母顺序排列(为了显示这一点，我将其中一些命名为 a- 和 c-tree)。
这是基本情节:
myplot <- ggplot(mydata, aes(x=sample, y=counts, fill=species))+
geom_bar(stat="identity", position = "fill") +
labs(x = "Samples", y = "Percentage of reads", fill = "Classification") +
theme(legend.position="bottom")
plot
所以我尝试了很多不同的东西，我发现堆栈溢出，但无法让它工作。
我认为，最有希望的方法是加入一个因素，例如:
mydata$group <- as.factor(mydata$group)
然后在图中添加一个子组:
myplot <- ggplot(mydata, aes(x=sample, y=counts, fill=species, subgroup=group))+
geom_bar(stat="identity", position = "fill") +
labs(x = "Samples", y = "Percentage of reads", fill = "Classification") +
theme(legend.position="bottom")
但这不会改变任何事情。而这只是给组添加颜色的第一步。
问题之一，为什么大多数关于堆栈溢出的答案是我有很多数据，而且并不是每个样本中都存在每个物种。所以我不能只给每个物种一个颜色。虽然我已经非常绝望了，我也尝试过，但由于某种原因它不起作用，无论如何这不是一种巧妙的方法......
非常感谢您的帮助!
最佳答案
更新 2
这是一种使用 hcl.colors 的方法，它也可以处理不按字母顺序排列的因素。此外，我使用 forcats::fct_relevel，以便物种按颜色深浅的顺序而不是 a-z 打印，参见 Factors with forcats Cheat Sheet
set.seed(1)
library("ggplot2")
library("tidyverse")
mydata <- data_frame(counts=c(560, 310, 250, 243, 124, 306, 1271, 112, 201, 305, 201, 304, 136, 211, 131 ),
species=c("zbact1", "bact1", "shrub1", "shrub1", "tree1", "tree1", "tree2", "algae1", "algae1", "bact2", "bact3", "tree3", "algae2", "shrub2", "shrub2"),
sample=c(1,2,1,1,2,2,1,1,2,2,2,2,1,1,2),
group=c("bacterium", "bacterium", "shrub", "shrub", "tree", "tree", "tree", "algae", "algae", "bacterium", "bacterium", "tree", "algae", "shrub", "shrub"))
#> Warning: `data_frame()` is deprecated, use `tibble()`.
#> This warning is displayed once per session.
mydata$species <- as.factor(mydata$species)
mydata$group <- as.factor(mydata$group)
make_pal <- function(group, sub){
stopifnot(
is.factor(group),
is.factor(sub)
)
# all the monochromatic pals in RColorBrewer
mono_pals <- c("Blues", "Greens", "Oranges", "Purples", "Reds", "Grays")
# how many sub levels per group level
data <- tibble(group = group, sub = sub) %>%
distinct()
d_count <- data %>%
count(group)
names_vec <- data %>%
arrange(group) %>%
magrittr::extract("sub") %>%
unlist
# make a named vector to be used with scale_fill_manual
l <- list(
n = d_count[["n"]],
name = mono_pals[1:length(levels(group))]
)
map2(l$n,
l$name,
hcl.colors) %>%
flatten_chr() %>%
set_names(names_vec)
}
custom_pal <- make_pal(mydata$group, mydata$species)
mydata$species <- fct_relevel(mydata$species, names(custom_pal))
myplot <- mydata %>%
ggplot(aes(x=sample, y=counts, fill=species))+
geom_bar(stat="identity", position = "fill") +
labs(x = "Samples", y = "Percentage of reads", fill = "Classification") +
scale_fill_manual(values = custom_pal)+
theme(legend.position="bottom")
myplot
创建于 2019-07-24 由 reprex package (v0.3.0)
关于r - 是否有 ggplot 函数用于为不同渐变的堆叠条形图中的子组着色？，我们在Stack Overflow上找到一个类似的问题： https://stackoverflow.com/questions/57148207/