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如何在gglpot2中定义y轴段

ggpubr facet ggplot2 r

John Gagnon · 技术社区 · 7 年前

我有一个数据框:

df <- structure(list(Sample = c("1: FL_643", "2: FL_645", "3: FL_647","4: FL_656", "5: FL_658", "6: cKO_644", "7: cKO_646", "8: cKO_654","9: cKO_655", "10: cKO_657", "1: FL_643", "2: FL_645", "3: FL_647", "4: FL_656", "5: FL_658", "6: cKO_644", "7: cKO_646", "8: cKO_654", "9: cKO_655", "10: cKO_657"), Genotype = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), .Label = c("miR-15/16 FL", "miR-15/16 cKO"), class = "factor"), 
Tissue = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Thymus", 
"iLN", "Spleen", "Skin", "Colon"), class = "factor"), variable = structure(c(1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L), .Label = c("Cells/SC/Live/CD8â,, CD4+,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3+,Freq. of Parent", "Cells/SC/Live/CD8â,, CD4+/Foxp3+,Median,<BV421-A>,CD127", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3+/CD25+,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3+/CD25-,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-,Freq. of Parent", "Cells/SC/Live/CD8â,, CD4+/Foxp3-,Median,<BV421-A>,CD127", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62Lâ,, CD44â,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62Lâ,, CD44+,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62L+,, CD44â,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62L+,, CD44+,Freq. of Parent", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD44+,Freq. of Parent", 
"Cells/SC/Live/CD8+,, CD4â,Freq. of Parent", "Cells/SC/Live/CD8+,, CD4â,Median,<BV421-A>,CD127", 
"Cells/SC/Live/CD8+,, CD4â/CD62Lâ,, CD44â,Freq. of Parent", 
"Cells/SC/Live/CD8+,, CD4â/CD62Lâ,, CD44+,Freq. of Parent", 
"Cells/SC/Live/CD8+,, CD4â/CD62L+,, CD44â,Freq. of Parent", 
"Cells/SC/Live/CD8+,, CD4â/CD62L+,, CD44+,Freq. of Parent", 
"Cells/SC/Live/CD8+,, CD4â/CD62L+,, CD44+,Freq. of Parent_1", 
"Cells/SC/Live,Count", "Cells/SC/Live/CD8â,, CD4+,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3+,Count", "Cells/SC/Live/CD8â,, CD4+/Foxp3+/CD25+,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3+/CD25-,Count", "Cells/SC/Live/CD8â,, CD4+/Foxp3-,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62Lâ,, CD44â,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62Lâ,, CD44+,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62L+,, CD44â,Count", 
"Cells/SC/Live/CD8â,, CD4+/Foxp3-/CD62L+,, CD44+,Count", 
"Cells/SC/Live/CD8+,, CD4â,Count", "Cells/SC/Live/CD8+,, CD4â/CD62Lâ,, CD44â,Count", 
"Cells/SC/Live/CD8+,, CD4â/CD62Lâ,, CD44+,Count", "Cells/SC/Live/CD8+,, CD4â/CD62L+,, CD44â,Count", 
"Cells/SC/Live/CD8+,, CD4â/CD62L+,, CD44+,Count"), class = "factor"), 
value = c(41.2, 35.5, 39.5, 33.2, 39.1, 35.5, 35.7, 33.9, 
39.7, 42.4, 10.9, 12.1, 10.9, 12.5, 12.3, 12.8, 14.1, 15.8, 
14.6, 12.5)), .Names = c("Sample", "Genotype", "Tissue", "variable", "value"), row.names = c(NA, -20L), class = "data.frame")

和am使用以下函数绘制数据的各种组合

library(ggplot2)
library(ggpubr)
plot_it <- function(Tissue,
                    row_add = (1:nrow(temp)), 
                    y.lab = "Did you forget to add a label?",
                    font_choice = "Helvetica",
                    font_size = 12,
                    stat_test = "t.test",
                    p_display = "p.signif",
                    legend_position = c("right")) {

  # Subset data frame based on row_add
  rownames(temp) <- NULL
  df <- droplevels(temp[c(row_add),])
  rownames(df) <- NULL
  View(temp)

  # Define color and shape of variables
  color.groups <- c("black","red")
  names(color.groups) <- unique(df$Genotype)
  shape.groups <- c(16, 1)
  names(shape.groups) <- unique(df$Genotype)

  # Generate data frame of reference y-values for p-value labels and bracket positions
  dmax = df %>% group_by(variable) %>% 
    summarise(value=max(value, na.rm=TRUE),
              Genotype=NA)

  # For tweaking position of brackets
  e = max(dmax$value)*0.1
  r = 0.6
  w = 0.19
  bcol = "black"

  # Define y axis and wrap label
  y.axis <- df$value
  y.lab <- str_wrap(y.lab, width = 40)

  ggplot(df, aes(x = variable, y = value, color = Genotype, shape = Genotype)) +
    # geom_violin(position = position_dodge(width = 0.75)) +
    geom_boxplot(position = position_dodge(width = 0.75), outlier.shape = NULL) +
    geom_point(position=position_dodge(width=0.75), size = 2) +
    ylim(0,1.2*max(y.axis, na.rm = TRUE)) + ylab(y.lab) + xlab(df$Tissue) +
    scale_color_manual(values=color.groups) +
    scale_shape_manual(values=shape.groups) +
    scale_x_discrete(labels = function(x) str_wrap(x, width = 20)) +
    theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"),
                       aspect.ratio = 1, text = element_text(family=font_choice, size = font_size),
                       legend.position = legend_position) +
    stat_compare_means(show.legend = FALSE, label = p_display, method = stat_test,
                       label.y = e + dmax$value, family = font_choice) +
    geom_segment(data=dmax,
                 aes(x=as.numeric(variable)-w, xend=as.numeric(variable)+w,
                     y=value + r*e, yend=value + r*e), size=0.3, color=bcol, inherit.aes=FALSE)
}

通过使用以下函数调用进行绘图:

plot_it(Tissue = "Thymus", row_add = c(c(1:30), c(141:150)))

我想让函数创建一个小平面包裹,将有效地将y轴转换为两段,以便两段的比例允许更好的数据可视化。事实上,当我用具有高度不同值的变量绘制图时,比例不适合所有这些变量。

如果这不可能,那么有没有一种简单的方法可以在每个绘图的基础上手动引入镶嵌面包裹来分解y轴?

1 回复 | 直到 7 年前

eipi10 7 年前

您可以使用聚类将具有相似手段的组保持在一起。然而,由于比例不同,这些图表可能会产生误导。

library(tidyverse)

# Fake data with five groups
set.seed(2)
dat = data.frame(group=rep(LETTERS[1:5], each=20),
                 sub=rep(rep(letters[1:2], each=10), 5),
                 value=rnorm(100, rep(c(20, 17, 27, 56, 80), each=20), 5))

# Add facet groups using kmeans clustering
dat = dat %>% 
  group_by(group) %>% 
  mutate(mean=mean(value)) %>% 
  ungroup %>% 
  mutate(facet_group = kmeans(mean, 2)$cluster)

ggplot(dat, aes(group, value, colour=sub)) +
  geom_boxplot() +
  facet_wrap(~ facet_group, scales="free", ncol=2) +
  expand_limits(y=0) +
  theme_classic() +
  theme(strip.background=element_blank(),
        strip.text=element_blank())

library(gridExtra)

# Create the two plots separately and store them in a list
plots = unique(dat$facet_group) %>% 
  map(
    ~ ggplot(dat[dat$facet_group==.x, ], aes(group, value, colour=sub)) +
      geom_boxplot() +
      expand_limits(y=0) +
      labs(y="", x="") +
      theme_bw() +
      theme(strip.background=element_blank(),
            strip.text=element_blank())
  )

# Extract Legend 
g_legend <- function(a.gplot) { 
  tmp <- ggplot_gtable(ggplot_build(a.gplot)) 
  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box") 
  legend <- tmp$grobs[[leg]] 
  return(legend)
  } 

leg = g_legend(plots[[1]])

# Lay out the plots and the legend
grid.arrange(
  arrangeGrob(grobs=map(plots, function(x) x + guides(colour=FALSE)), widths=c(3,2)),
  leg, widths=c(10,1), left="Value", bottom="Group"
  )