Lesson 05 for Plotting in R for Biologists

Last updated on 3 min read Visualization

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这节课作者命名为"Tweaking everything in a plot"。主要是对图形细节进行优化，包括：

  • 题目(title)、坐标轴标签、图例标签等
  • 字体
  • 颜色
  • 背景
  • 网格线等

数据加载及清洗

这部分在上节课已经讲过了，这里就不再详述了。

library(tidyverse)
library(plyr)
my_data <- read.csv("Encode_HMM_data.txt", sep = "\t", header = FALSE)
names(my_data)[1:4] <- c("chrom","start","stop","type")
my_data$chrom <- factor(gsub("chr","", my_data$chrom, fixed = TRUE), levels = c(seq(1:22),"X","Y"))
my_data <- my_data[my_data$type %in% c("1_Active_Promoter","4_Strong_Enhancer","8_Insulator"), ]
my_data$type <- revalue(my_data$type, c("1_Active_Promoter"="Promoter", "4_Strong_Enhancer"="Enhancer","8_Insulator"="Insulator"))

可视化

接下来就针对图形进行优化调整

ggplot(my_data, aes(x=chrom, fill=type))+geom_bar()

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添加标题

ggplot(my_data, aes(x=chrom, fill=type))+geom_bar()+labs(title="Regulatory features by chromosomes")

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需要注意的一点是，添加的title默认是位于左上角，如果要居中显示的话最简单的办法就是在标题前添加空格。

修改坐标轴以及图例标签

ggplot(my_data, aes(x=chrom, fill=type))+
  geom_bar()+
  labs(x="Chromosome", y="Count", fill="Feature")#这里fill是对应ampping里面的fill映射，显示于图例

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主题修改

basic <- ggplot(my_data, aes(x=chrom, fill=type))+
  geom_bar()+
  labs(x="Chromosome", y="Count", fill="Feature")
#设置文本大小
(basic+theme_gray(base_size = 20))

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如果想要使得主题适用于所有的图形，可以通过theme_set()进行设置。

theme_set(theme_gray(base_size = 20))
basic

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恢复默认设置主题

theme_set(theme_gray())
basic

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颜色

R有个包RColorNBrewer提供调色板

library(RColorBrewer)
display.brewer.all()

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下面测试一下这些调色板

basic+scale_fill_brewer(palette = "Set1")

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basic+scale_fill_brewer(palette = "Pastel1")

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basic+scale_fill_brewer(palette = "YlorRd")

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不使用调色板的话也可以自己设置颜色，结合取色器的话很是很赞的

basic+scale_fill_manual(values = c("green", "blue", "red"))

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head(colors())

## [1] "white"         "aliceblue"     "antiquewhite"  "antiquewhite1"
## [5] "antiquewhite2" "antiquewhite3"

有的时候我们需要很多种颜色，多到一个调色板都满足不了时怎么办？

chrom_plot <- ggplot(my_data, aes(x=type, fill=chrom))+geom_bar()
chrom_plot

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chrom_plot+scale_fill_brewer(type = "qual", palette = 1)

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ggplot默认调用的是rainbpw调色板，颜色容易让人误解，不好分辨，但是其他的调色板颜色数量是不足的。这时可以通过将好几个palette合并在一起组成一个新的palette。

palette1 <- brewer.pal(9, "Set1")
palette1

## [1] "#E41A1C" "#377EB8" "#4DAF4A" "#984EA3" "#FF7F00" "#FFFF33" "#A65628"
## [8] "#F781BF" "#999999"

palette2 <- brewer.pal(8, "Set2")
palette2

## [1] "#66C2A5" "#FC8D62" "#8DA0CB" "#E78AC3" "#A6D854" "#FFD92F" "#E5C494"
## [8] "#B3B3B3"

palette3 <- brewer.pal(9, "Set3")
palette3

## [1] "#8DD3C7" "#FFFFB3" "#BEBADA" "#FB8072" "#80B1D3" "#FDB462" "#B3DE69"
## [8] "#FCCDE5" "#D9D9D9"

通过饼图来查看一下这几个调色板

pie(rep(1, length(palette1)), col = palette1)

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pie(rep(1, length(palette2)), col = palette2)

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pie(rep(1, length(palette3)), col = palette3)

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将这几个色斑合并成一个大的调色板

big_palette <- c(palette1, palette2, palette3)
pie(rep(1, length(big_palette)), col = big_palette)

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chrom_plot+scale_fill_manual(values = big_palette)

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也可以打乱颜色顺序

chrom_plot+scale_fill_manual(values = sample(big_palette))

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字体

后续大部分调整都是通过theme来实现的。

#对所有字体进行调整
basic+theme_gray(base_size = 24, base_family = "Times New Roman")

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但是很多时候我们都是对特定字体、标签、颜色等进行特定的调整，这时就可以通过theme逐一调整。

basic+theme(axis.text = element_text(size=20))

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basic+theme(axis.title = element_text(size = 20))

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basic+theme(legend.title = element_text(size = 20))

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basic+theme(legend.text = element_text(size=20, family = "Times New Roman"))

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basic+theme(legend.text = element_text(size=20, family = "Times New Roman"),
            axis.title = element_text(size=30),
            axis.text = element_text(size=20))

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背景

basic+theme(panel.background = element_rect(fill="pink"))

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basic+theme(panel.background = element_rect(fill="white"))

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网格线

basic+theme(panel.grid.major = element_line(colour = "blue"), panel.grid.minor = element_line(colour = "red"))

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移除所有的网格线

basic+theme(panel.grid.major = element_line(NA),
            panel.grid.minor = element_line(NA))

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只保留y轴线

basic+theme(panel.grid.major.y = element_line(colour = "black", size = 0.20),
            panel.grid.major.x = element_line(NA),
            panel.grid.minor = element_line(NA))

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修改刻度

basic+theme(axis.ticks = element_line(size=0.2))

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basic+theme(axis.ticks = element_line(NA))

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basic+theme(axis.ticks = element_line(colour = "blue", size = 2))

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basic+theme(axis.ticks = element_line(size=2),
            axis.ticks.x = element_line(colour = "blue"),
            axis.ticks.y = element_line(colour = "red"))

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图例

修改图例位置

basic+theme(legend.position = "top")

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basic+theme(legend.position = "bottom")

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basic+theme(legend.position = c(0,0))#左下角

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basic+theme(legend.position = c(1,1))#右上角

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basic+theme(legend.position = c(0.8,0.8))#通过坐标设置可以将图例置于任意位置

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移除图例

basic+labs(fill="")

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basic+labs(fill="")+theme(legend.position = c(0.8,0.8))

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看看文章发表样式图形

publication_style <- basic+guides(fill=FALSE)+
  theme(axis.line = element_line(size = 0.5), 
        panel.background = element_rect(fill=NA, size = rel(20)),
        panel.grid.minor = element_line(colour = NA),
        axis.text = element_text(size=16),
        axis.title = element_text(size = 18))
publication_style

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将柱形图与x轴之间的距离消除

publication_style+scale_y_continuous(expand = c(0,0))

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可以看到上述图形基本达到了文章发表的水平，因此我们可以将主题theme保存下来以后使用，通过设置全局主题来使所有图形有相同版式。

theme_set(theme_gray()+
            theme(axis.line = element_line(size = 0.5),
                  panel.background = element_rect(fill=NA, size = rel(20)),
                  panel.grid.minor = element_line(colour = NA),
                  axis.text = element_text(size = 16),
                  axis.title = element_text(size = 18)))
basic

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basic+scale_y_continuous(expand = c(0,0))+guides(fill=FALSE)

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如果需要还原主题设定的话，只要运行以下命令就行：

theme_set(theme_gray())

SessionInfO()

sessionInfo()

## R version 3.4.3 (2017-11-30)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 16299)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936 
## [2] LC_CTYPE=Chinese (Simplified)_China.936   
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C                              
## [5] LC_TIME=Chinese (Simplified)_China.936    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] RColorBrewer_1.1-2 plyr_1.8.4         forcats_0.2.0     
##  [4] stringr_1.2.0      dplyr_0.7.4        purrr_0.2.4       
##  [7] readr_1.1.1        tidyr_0.7.2        tibble_1.4.2      
## [10] ggplot2_2.2.1.9000 tidyverse_1.2.1   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.15      cellranger_1.1.0  pillar_1.1.0     
##  [4] compiler_3.4.3    bindr_0.1         tools_3.4.3      
##  [7] digest_0.6.14     lubridate_1.7.1   jsonlite_1.5     
## [10] evaluate_0.10.1   nlme_3.1-131      gtable_0.2.0     
## [13] lattice_0.20-35   pkgconfig_2.0.1   rlang_0.1.6      
## [16] psych_1.7.8       cli_1.0.0         rstudioapi_0.7   
## [19] yaml_2.1.16       parallel_3.4.3    haven_1.1.1      
## [22] bindrcpp_0.2      xml2_1.2.0        httr_1.3.1       
## [25] knitr_1.18        hms_0.4.1         rprojroot_1.3-2  
## [28] grid_3.4.3        glue_1.2.0        R6_2.2.2         
## [31] readxl_1.0.0      foreign_0.8-69    rmarkdown_1.8    
## [34] modelr_0.1.1      reshape2_1.4.3    magrittr_1.5     
## [37] backports_1.1.2   scales_0.5.0.9000 htmltools_0.3.6  
## [40] rvest_0.3.2       assertthat_0.2.0  mnormt_1.5-5     
## [43] colorspace_1.3-2  labeling_0.3      stringi_1.1.6    
## [46] lazyeval_0.2.1    munsell_0.4.3     broom_0.4.3      
## [49] crayon_1.3.4
Biologists
Researcher

I am a PhD student of Crop Genetics and Breeding at the Zhejiang University Crop Science Lab. My research interests covers a range of issues:Population Genetics Evolution and Ecotype Divergence Analysis of Oilseed Rape, Genome-wide Association Study (GWAS) of Agronomic Traits.

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