如何使用ggrepel或其他方式对齐和标记ggalluvial中的地层

问题描述

我在 R 中使用 ggalluvial 生成了一些冲积图。

下面的代码示例产生了接近我想要实现的目标。例如，

library("ggalluvial")
par(mar = c(1,1,1)*12,cex = 0.6,xpd=NA)

# generate some example data
somelongnames <- c("homo sapiens","homo sapiens",letters[18],"some other long name",letters[seq(4)])

df <- data.frame(x = factor(somelongnames),y = factor(c("this label is long","Golgi",letters[13:18])),count = c(2,10,4,5,9,3))

ll <- unique(c(as.character(df$x),as.character(df$y)))
grid.col <- rainbow(length(ll))
grid.col <- setNames(grid.col,ll)

# set colours for alluvial plot (this is a little tricky as strata 
# colour ordering is required for ggalluvial strata)
names(df) <- c("Condition1","Condition2","value")
levs1 <- levels(df$Condition1) 
levs2 <- levels(df$Condition2)
res1 <- unique(df$Condition1)
res2 <- unique(df$Condition2)
cond1_cols <- grid.col[levs1[levs1 %in% res1]]
cond2_cols <- grid.col[levs2[levs2 %in% res2]]
columnCols <- c(cond1_cols,cond2_cols)
stratCols <- c(rev(cond1_cols),rev(cond2_cols))

# plot alluvial diagram
q <- ggplot(df,aes(y = value,axis1 = Condition1,axis2 = Condition2)) +
  geom_alluvium(aes(fill = Condition1),width = 0) +
  scale_fill_manual(values = columnCols) +
  geom_stratum(width = 1/8,fill = paste0(stratCols),color = "white") +
  scale_x_discrete(limits = c("Condition1","Condition2"),expand = c(.09,.09)) +
  scale_y_continuous(breaks = NULL) +
  theme_minimal() +
  theme(axis.ticks.y = element_blank(),axis.text.y = element_blank(),panel.grid.major.y = element_blank(),panel.grid.major.x = element_blank()) +
  theme(legend.position = "none") +
  ylab(NULL)

# add labels
  q +
    geom_label(stat = "stratum",aes(label = after_stat(stratum)),color = stratCols,fontface = "bold",size = 3)     

我想移动标签，使它们位于地层的左侧和右侧，这样它们就不会与情节重叠（当标签很长时，这尤其令人讨厌）。我见过使用 ggrepel 包执行此操作的示例。

我尝试在 ifelse 中对 aes 的调用中使用 for 循环和 geom_text_repel 语句（按照 Solution 2 here），但无法弄清楚代码.任何人都可以提供帮助或有更好的解决方案来实现这一目标吗？

使用 ggrepel 的失败代码示例，例如

q + ggrepel::geom_text_repel(
    aes(label = ifelse(Condition1 == as.character(res1)[1],as.character(res1)[1],NA)),stat = "stratum",size = 4,direction = "y",nudge_x = -.5
) 

理想情况下，我希望在此示例中由 Jason Cory Brunson 生成类似 solution 2 的内容。

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  Grdevices utils     datasets  methods   base     

other attached packages:
 [1] ggalluvial_0.12.3    RColorBrewer_1.1-2   archivist_2.3.6      circlize_0.4.12      dplyr_1.0.5          viridis_0.6.0       
 [7] viridisLite_0.4.0    pheatmap_1.0.12      pRolocdata_1.29.1    ggplot2_3.3.3        bandle_1.0           pRoloc_1.30.0       
[13] BiocParallel_1.24.1  MLInterfaces_1.70.0  cluster_2.1.1        annotate_1.68.0      XML_3.99-0.6         AnnotationDbi_1.52.0
[19] IRanges_2.24.1       MSnbase_2.16.1       ProtGenerics_1.22.0  mzR_2.24.1           Rcpp_1.0.6           Biobase_2.50.0      
[25] S4Vectors_0.28.1     Biocgenerics_0.36.0  BiocStyle_2.18.1    

解决方法

也许这符合您的需要。第一的。由于我对 ggalluvial 不太熟悉，因此我更改了数据设置以遵循链接中示例中的代码，首先扩展数据集并将其转换为长格式。这样做使我能够在 stratum 和 alluvium aes 上制作地图，并可以更轻松地以 Condition 变量为条件。

这样做之后，您可以使用默认的 geom_text 通过使用 ifelse 来对齐标签。或者您可以使用两个 geom_text_repel 层将标签放在层的左侧或右侧。

library(tidyr)
library(dplyr)

df_expanded <- df[rep(row.names(df),df$value),]
df_expanded <- df_expanded %>%
  mutate(id = row_number()) %>%
  pivot_longer(-c(value,id),names_to = "Condition",values_to = "label")

# plot alluvial diagram
q <- ggplot(df_expanded,aes(x = Condition,stratum = label,alluvium = id,fill = label)) +
  geom_flow(width = 0) +
  scale_fill_manual(values = columnCols) +
  scale_color_manual(values = stratCols) +
  geom_stratum(width = 1 / 8,color = "white") +
  scale_x_discrete(
    expand = c(.25,.25)
  ) +
  scale_y_continuous(breaks = NULL) +
  theme_minimal() +
  theme(
    axis.ticks.y = element_blank(),axis.text.y = element_blank(),panel.grid.major.y = element_blank(),panel.grid.major.x = element_blank()
  ) +
  theme(legend.position = "none") +
  ylab(NULL)

q +
  geom_text(
    aes(
      label = after_stat(stratum),hjust = ifelse(Condition == "Condition1",1,0),x = as.numeric(factor(Condition)) + .075 * ifelse(Condition == "Condition1",-1,1),color = after_stat(stratum)
    ),stat = "stratum",fontface = "bold",size = 3
  )
#> Warning: The `.dots` argument of `group_by()` is deprecated as of dplyr 1.0.0.

q +
  ggrepel::geom_text_repel(
  aes(label = ifelse(after_stat(x) == 1,as.character(after_stat(stratum)),"")),size = 4,direction = "y",nudge_x = -.6) +
  ggrepel::geom_text_repel(
    aes(label = ifelse(after_stat(x)  == 2,nudge_x = .6
  )