使用 jjAnno 对分面添加注释

Original JunJunLab 老俊俊的生信笔记 2023-09-04

收录于合集 #R包分享 178个

风萧萧兮易水寒

1引言

其实分面和添加注释有着异曲同工之妙,都是 对数据进行分组添加说明。那么是不是添加了分类注释,分面就可以抛弃了了呢? 其实不然,分面当然还有其它作用,例如把不同组的数据分开展示,同时还要 展示组内数据之间的相对差异, 去除不同组别之间极值对数据的展示影响, 这时我们可以设置 scales = 'free_x/y' 参数达到目的。

新功能:

支持对分面图形添加注释。

支持的函数:

annoPoint2
annoSegment
annoRect
annoTriangle

Note:

如果你使用 facet_grid 同时对 X 和 Y 轴都进行了分面,那么再添加注释是没有什么意义了,反而显得冗余,所以这里 只支持 X 或 Y 的分面图形添加注释。
此外需要注意的是,绘图的时候你需要把映射的变量放在 其它对应的 geom 图层里, 而不是 ggplot 函数里面,否则会报错,例如ggplot(dot_data)而不是ggplot(dot_data,aes(x = gene,y = cell))。

安装:

如果你想获得新的功能,重新安装即可:

# install.packages("devtools")
devtools::install_github("junjunlab/jjAnno")

library(jjAnno)

参考手册地址:

https://junjunlab.github.io/jjAnno-manual/facet-introduction.html

2basic plot

library(jjAnno)
library(tidyverse)
library(ggplot2)

# load data
dot_data <- read.delim('gene-dot.txt',header = T) %>%
  arrange(class)

# add cell group
dot_data$cellGroup <- case_when(
  dot_data$cell %in% c("1b CoelEpi GATA4", "2a Early somatic", "2b ESGC male") ~ "cell type1",
  dot_data$cell %in% c("2b ESGC female", "2c PreGC-I", "2d Sertoil")  ~ "cell type2",
  dot_data$cell %in% c("3a Early sPAX8", "3b Gi")  ~ "cell type3"
)

# order
dot_data$gene <- factor(dot_data$gene,levels = unique(dot_data$gene))

# plot
pdotfc <-
  # ggplot(dot_data,aes(x = gene,y = cell)) +
  ggplot(dot_data) +
  geom_point(aes(fill = mean.expression,size = percentage,
                 x = gene,y = cell
  ),
  color = 'black',
  shape = 21) +
  theme_bw(base_size = 14) +
  xlab('') + ylab('') +
  scale_fill_gradient2(low = 'white',mid = '#EB1D36',high = '#990000',
                       midpoint = 0.5,
                       name = 'Mean expression') +
  scale_size(range = c(1,8)) +
  theme(panel.grid = element_blank(),
        axis.text = element_text(color = 'black'),
        # aspect.ratio = 0.5,
        plot.margin = margin(t = 2,r = 1,b = 1,l = 1,unit = 'cm'),
        axis.text.x = element_text(angle = 90,hjust = 1,vjust = 0.5,
                                   face = 'italic')) +
  coord_cartesian(clip = 'off')

pdotfc

Or load test data directly:

data(pdotfc)

3annoPoint2

facet by cellGroup

Let's see a facet example:

# facet by cellGroup
pfacet <-
  pdotfc +
  facet_wrap(~cellGroup,
             ncol = 1,scales = 'free_y',
             strip.position = 'right')

pfacet

Trying to add point annotation:

# add to top
annoPoint2(object = pfacet,
           annoPos = 'top',
           aesGroup = T,
           aes_x = 'gene',
           aes_y = 'cell',
           aesGroName = 'class',
           myFacetGrou = 'cell type1',
           ptSize = 2,
           yPosition = 4.2)

It seems that the annoPoint2 function works well! Here remember that you should supply the X and Y mapping variables with aes_x and aes_y. Also you need to point out which variable(aesGroName) and sub-facet group name(myFacetGrou) should be used to add an annotation.

If you want to add to the bottom, just change the myFacetGrou:

# change cellGroup and add to botomn
annoPoint2(object = pfacet,
           annoPos = 'botomn',
           aesGroup = T,
           aes_x = 'gene',
           aes_y = 'cell',
           aesGroName = 'class',
           myFacetGrou = 'cell type3',
           yPosition = -0.6,
           ptSize = 2)

facet by class

Facet by another group:

# facet by class
pfacet1 <-
  pdotfc +
  facet_wrap(~class,
             nrow = 1,scales = 'free_x') +
  theme(axis.text.y = element_text(margin = margin(r = 1.2,unit = 'cm')))

pfacet1

Adding to left:

# add to left
annoPoint2(object = pfacet1,
           annoPos = 'left',
           aesGroup = T,
           aes_x = 'gene',
           aes_y = 'cell',
           aesGroName = 'cellGroup',
           myFacetGrou = 'Early supporting',
           ptSize = 2,
           xPosition = -0.5,
           pCol = rep(useMyCol('paired',3),c(3,3,2)))

4annoSegment

Let's see examples for annoSegment.

facet by cellGroup

# facet by cellGroup
pfacet <-
  pdotfc +
  facet_wrap(~cellGroup,
             ncol = 1,scales = 'free_y',
             strip.position = 'right') +
  theme(plot.margin = margin(t = 5,unit = 'cm'))

# add segment to top
annoSegment(object = pfacet,
            annoPos = 'top',
            aesGroup = T,
            aes_x = 'gene',
            aes_y = 'cell',
            aesGroName = 'class',
            myFacetGrou = 'cell type1',
            yPosition = 4.2,
            segWidth = 0.8,
            lwd = 4,
            mArrow = arrow(ends = 'both',length = unit(0.25,'cm')),
            addText = T,
            textRot = 45,
            textHVjust = 0.5,
            hjust = 0)

You can also add to the middle facet group:

# add segment to "cell type2" top
annoSegment(object = pfacet,
            annoPos = 'top',
            aesGroup = T,
            aes_x = 'gene',
            aes_y = 'cell',
            aesGroName = 'class',
            myFacetGrou = 'cell type2',
            yPosition = 4,
            segWidth = 0.8) +
  theme(panel.spacing.y = unit(1,'cm'))

facet by class

# facet by class
pfacet1 <-
  pdotfc +
  facet_wrap(~class,
             nrow = 1,scales = 'free_x') +
  theme(axis.text.y = element_text(margin = margin(r = 1.2,unit = 'cm')))

# add segment to left
annoSegment(object = pfacet1,
            annoPos = 'left',
            aesGroup = T,
            aes_x = 'gene',
            aes_y = 'cell',
            aesGroName = 'cellGroup',
            myFacetGrou = 'Early supporting',
            xPosition = -0.5,
            segWidth = 0.8,
            lwd = 4,
            addBranch = T,
            branRelSegLen = 0.8,
            bArrow = arrow(length = unit(0.3,'cm')))

5annoRect

Let's see examples for annoRect.

facet by cellGroup

# facet by cellGroup
pfacet <-
  pdotfc +
  facet_wrap(~cellGroup,
             ncol = 1,scales = 'free_y',
             strip.position = 'right') +
  theme(plot.margin = margin(t = 5,b = 4,unit = 'cm'),
        axis.text.x = element_text(angle = 60,hjust = 1,vjust = 1))

# add rect to top
annoRect(object = pfacet,
         annoPos = 'top',
         aesGroup = T,
         aes_x = 'gene',
         aes_y = 'cell',
         aesGroName = 'class',
         myFacetGrou = 'cell type1',
         yPosition = c(4,4.6),
         rectWidth = 0.8,
         pCol = rep('black',11),
         lwd = 2,
         addText = T,
         textRot = 45,
         textHVjust = 0.6,
         hjust = 0)

Adding to bottom:

# add rect to botomn
annoRect(object = pfacet,
         annoPos = 'botomn',
         aesGroup = T,
         aes_x = 'gene',
         aes_y = 'cell',
         aesGroName = 'class',
         myFacetGrou = 'cell type3',
         yPosition = c(-1.2,0.4),
         rectWidth = 0.9,
         alpha = 0.5)

Roate the rect:

# add rotated rect to botomn
annoRect(object = pfacet,
         annoPos = 'botomn',
         aesGroup = T,
         aes_x = 'gene',
         aes_y = 'cell',
         aesGroName = 'class',
         myFacetGrou = 'cell type3',
         yPosition = c(-1.5,0.3),
         rectWidth = 0.9,
         alpha = 0.5,
         rotateRect = T,
         rectAngle = 50,
         rotatedRectShift = 0.75)

facet by class

# facet by class
pfacet1 <-
  pdotfc +
  facet_wrap(~class,
             nrow = 1,scales = 'free_x') +
  theme(axis.text.y = element_text(margin = margin(l = 1,unit = 'cm')))

# add to left
annoRect(object = pfacet1,
         annoPos = 'left',
         aesGroup = T,
         aes_x = 'gene',
         aes_y = 'cell',
         aesGroName = 'cellGroup',
         myFacetGrou = 'Early supporting',
         xPosition = c(-6,0.2),
         rectWidth = 0.9,
         alpha = 0.3)

6annoTriangle

Let's see examples for annoRect.

facet by cellGroup

# facet by cellGroup
pfacet <-
  pdotfc +
  facet_wrap(~cellGroup,
             ncol = 1,scales = 'free_y',
             strip.position = 'right')

# add rect to top
annoTriangle(object = pfacet,
             annoPos = 'top',
             aes_x = 'gene',
             aes_y = 'cell',
             myFacetGrou = 'cell type1',
             xPosition = c(1,21),
             yPosition = c(4,4.6),
             fillCol = c('blue','white','red'))