如何用对应于相对丰度图的颜色标签制作复合图例？

如何解决如何用对应于相对丰度图的颜色标签制作复合图例？

我想复制以下paper中的图形。

Fig.1c

它被卡在分隔X1列上。我想使用正则表达式，但不知道如何使用。我有一个计划，用下划线分隔符分隔每个单词（我有一个列表），然后分别将[-tes＆-ria]和[-ceae]后缀单词提取到Phylum和Family中。在那之后，家庭之后的话应该被归为属。为了准确起见，可能会将“未分类”和少于5个字符的单词的条件分组到前面的单词。

还有，是否可以在每个家族中添加与相对丰度图相对应的小颜色标签？

library(tidyverse)
james <- read_csv("tableS2a.csv")
james <- james %>% mutate(
    Cecum = rowSums(select(james,contains("Caecum"))),Transverse = rowSums(select(james,contains("Transv"))),Sigmoid = rowSums(select(james,contains("Sigmoi")))
  )
james2 <- james %>% 
  select(X1,Cecum,Transverse,Sigmoid) 

james.tab <- james2 %>%
  mutate(meanAbundance = 
           rowMeans(
             column_to_rownames(james2,var = "X1")
             )
         ) %>%
  arrange(desc(meanAbundance)) %>%
  top_n(30,meanAbundance) # extract top30

write.csv2(james.tab,"jamestab.csv")

james.tab2 <- 
  as.data.frame(
    apply(
      select(
        james.tab,Sigmoid),2,function(x) x / sum(x) * 100)
    )

james.tab3 <-
  bind_cols(
    as.data.frame(
      select(james.tab,X1)),as.data.frame(james.tab2)
    )

james.X1 <- select(james.tab3,X1)

# Separate X1 to Phylum(-tes/-ria),Family (-ceae),and genus
james.list <- strsplit(pull(james.X1,X1),"_")
james.class <-
  if_else(grepl("(ceae)",james.X1) == T,mutate(james.X1,Family =
                   grep(
                     "[[:alpha:]]ceae(_)",strsplit(pull(james.X1,"_"),value = T
                   )))

我是R的新手，上面的代码大部分是我以前的工作中粘贴的。如果代码效率低下，请原谅我。数据集：Original table-> Top30 csv (pastebin)

APPEND

这是最近的结果我没有成功实现ggtext包，可能是主题地址错误？

library(tidyverse)
library(patchwork)
library(ggtext)
library(glue)

james <- read_csv("tableS2a.csv")
james2 <- james %>% 
  mutate(
  Cecum = rowSums(select(james,contains("Sigmoi")))
  ) %>% 
  select(X1,Sigmoid) %>% 
  filter(grepl("(ceae)",james$X1)) # Filter rows with -ceae suffix only

# extract family value with selecting -ceae/les suffix word
family.naming0 <-
  regmatches(james2$X1,regexpr("(?<=_)(.*?(ceae|les)(?=_))",james2$X1,perl = T))
#in between "_" to fail-safe double -ceae. E.g. Bacteria_Bacteriaceae_Aceae

family.naming1 <-
  regmatches(james2$X1,regexpr("(?<=ceae_|les_)\\d",perl = T))

family.naming2 <- 
  regmatches(james2$X1,regexpr("(?<=ceae_|les_)unclassified",perl = T))

family.naming3 <-
  ifelse(
    grepl("(?<=[(ceae_)|(les_)])\\d",perl = T),paste0(family.naming0," ",family.naming1),ifelse(
      grepl("(?<=[(ceae_)|(les_)])unclassified",family.naming2),paste0(family.naming0)
    ))  

james3 <- james2 %>% 
  gather("Cecum","Transverse","Sigmoid",key = "location",value = "abundance") %>% 
  mutate(relativeAbundance=abundance/sum(abundance) * 100) %>%
  mutate(phylum=gsub("(_.*)","",X1)) %>% # extract phylum value with selecting first word
  mutate(family=
           ifelse(
             grepl("(?<=[(ceae_)|(les_)])\\d",X1,ifelse(
               grepl("(?<=[(ceae_)|(les_)])unclassified",paste0(family.naming0)
             ))) %>% 
  mutate(genus=gsub("_",sub("(.*ceae)+?_((unclassified|\\d)*(_)*)",X1)))

# change it into percentage
james4 <-
  bind_cols(select(james2,as.data.frame(
    apply(
      select(
        james2,function(x) x / sum(x) * 100)))

jamesReg <- james4 %>% 
  mutate(james4,meanAbundance=rowMeans(select(james4,Sigmoid))) %>% 
  arrange(desc(meanAbundance)) %>% 
  top_n(30,meanAbundance) %>% 
  pull(X1)

# collect top 30 from james4X reference
james5 <- james3 %>% 
  filter(X1 %in% jamesReg)

# change order
james5$location_f <- 
  factor(james5$location,labels = c("Cecum","Sigmoid"))

james6 <- 
  select(james5,location_f,relativeAbundance,genus)

# First plot
james.plot <-
  ggplot(james6,aes(x = location_f,y = relativeAbundance,fill = genus)) +
  geom_bar(position = "fill",stat = "identity",show.legend = F) +
  scale_y_continuous(labels = scales::percent_format(accuracy = 1)) + # y axis percentage
  #theme_minimal() +
  theme(axis.title.x = element_blank(),panel.background = element_blank()) +
  ylab("Relative abundances (%)") +
  scale_fill_hue(l=60,c=80)


james.table <- data.frame("relativeAbundance"=james5$relativeAbundance[1:30]+
                            james5$relativeAbundance[31:60]+
                            james5$relativeAbundance[61:90],"phylum"=james5$phylum[1:30],"family"=james5$family[1:30],"genus"=james5$genus[1:30])

# get colour pattern 
ggplotColours <- function(n = 6,h = c(0,360) + 15) {
  if ((diff(h) %% 360) < 1)
    h[2] <- h[2] - 360 / n
  hcl(h = (seq(h[1],h[2],length = n)),c = 100,l = 65)
}

family <- pull(select(james.table,family))
genus <- pull(select(james.table,genus))
james.table2 <- james.table %>% 
  mutate(color=ggplotColours(nrow(james.table))) %>% # just in case 
  mutate(asv=glue("{family}: <i>{genus}</i>"))

# color for long vertical tile (phylum tile)
james.phyl.col <- c("#fddb47","#58b9b2","#6585c3","#e25a4b")

# legend making or second plot
james.legend <- 
  ggplot(james.table2,aes(y = asv)) +
  geom_tile(aes(x = 1,fill = asv),width = 0.9,height = 0.9) +
  geom_tile(aes(x = 0.2),fill = james.phyl.col[as.numeric(as.factor(james.table2$phylum))],width = 0.4) +
  scale_y_discrete(position = "right",expand = c(0,0),name = "") +
  scale_x_continuous(expand = c(0,breaks = NULL,name = "") +
  scale_fill_discrete(guide = "none") +
  facet_grid(phylum ~ .,scales = "free_y",space = "free_y",switch = "y") +
  theme(axis.ticks = element_blank(),strip.background = element_blank(),aspect.ratio = 1,axis.text.y = element_markdown())

# patchwork
james.plot + james.legend

最终图片final

解决方法

这是一个示例，说明如何开始将图例制作为单独的图，以后可以将其拼凑到主图旁边。

基本上，您要为每个项目制作图块，然后按组对其进行分面。使刻面与刻面的比例完全为1：1有点棘手，因此您必须使用width = ...和height = ...来使其看起来正确。

library(ggplot2)

# Example of item-group relations
df <- data.frame(
  group = c("Actinobacteria","Actinobacteria","Bacteroidetes","Firmicutes","Firmicutes"),item = c("Bifidobacteriaceae","Coriobacteriaceae","Bacteroidaceae","Porphyromonadacea","Acidaminococcacaea","Clostridiacea","Clostridiales")
)

group_colours <- c("blue","green","red")

ggplot(df,aes(y = item)) +
  geom_tile(aes(x = 1,fill = item),width = 0.9,height = 0.9) +
  geom_tile(aes(x = 0.2),fill = group_colours[as.numeric(as.factor(df$group))],width = 0.4) +
  scale_y_discrete(position = "right",expand = c(0,0),name = "") +
  scale_x_continuous(expand = c(0,breaks = NULL,name = "") +
  scale_fill_discrete(guide = "none") +
  facet_grid(group ~ .,scales = "free_y",space = "free_y",switch = "y") +
  theme(axis.ticks = element_blank(),strip.background = element_blank(),aspect.ratio = 1)

^{由reprex package（v0.3.0）于2020-08-18创建}

如何用对应于相对丰度图的颜色标签制作复合图例？

如何解决如何用对应于相对丰度图的颜色标签制作复合图例？

解决方法

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