如何使用ggplot2制作多面的箱线图

Question

我有以下数据框：

samples_i <- c("LAIV D0", "LAIV D3", "LAIV D7", "LAIV D0", "LAIV D3", "LAIV D7", 
"TIV D0", "TIV D3", "TIV D7", "TIV D0", "TIV D3", "TIV D7")

irisTag_i <- structure(c(0, 0, 0, 11.2672863636364, 0, 0, 0, 0, 0, 0, 13.8881727272727, 
0, 0, 0), .Dim = c(2L, 7L), .Dimnames = list(c("HSP90B1", "DNAJB1"
), c("Neutrophil", "Tcell", "Monocyte", "Bcell", "NKcell", "PlasmaCell", 
"DendriticCell")))


SPVsR_i <- structure(c(0.1620678925564, -0.0609851972808482, -0.101082695275552, 
0.184268723991321, -0.0899021067853178, -0.0943666172060028, 
0.178289177586651, -0.0823892768809311, -0.0958999007057199, 
0.0331377432233005, 0.00289013805790048, -0.036027881281201, 
-0.0531973808347148, 0.0213528550009522, 0.0318445258337625, 
0.0179790366380429, 0.00347902775389391, -0.0214580643919368, 
-0.0136820170970586, 0.0142833182813199, -0.000601301184261278, 
0.0109856660204762, -0.00528600624634141, -0.00569965977413478, 
-0.0760171167711921, 0.0344372228755224, 0.0415798938956697, 
-0.114239469843063, 0.0217218301803764, 0.0925176396626868, -0.113283279031257, 
0.0424936766667866, 0.07078960236447, -0.14127024964406, 0.0595080054464686, 
0.0817622441975909, -0.0100499090500894, 0.0131491664210288, 
-0.00309925737093941, 0.101206058442775, 0.0231964804556542, 
-0.124402538898429, 0.00411785437964246, 0.0405556634613935, 
-0.044673517841036, 0.0720705616752313, -0.00782701824901867, 
-0.0642435434262126, 0.0753224665976433, -0.0323083061719772, 
-0.0430141604256661, -0.0654080281579984, 0.0124273486220488, 
0.0529806795359496, -0.0519970799923912, 0.00818146905729871, 
0.0438156109350925, 0.0200682008260364, -0.0466408267852637, 
0.0265726259592274, -0.0390251373720762, -0.0115216989414941, 
0.0505468363135703, 0.0321298528741327, -0.0151866963239294, 
-0.0169431565502034, -0.0310600302048482, 0.00718748395053659, 
0.0238725462543116, -0.0216937374381297, -0.00559429498828404, 
0.0272880324264137, 0.0288166559498562, -0.0173984873138801, 
-0.0114181686359761, -0.0176892628883129, -0.0235673738231865, 
0.0412566367114994, -0.00794904064609583, -0.000656094604392996, 
0.00860513525048881, -0.0538196455977893, 0.0200107051556589, 
0.0338089404421304), .Dim = c(12L, 7L), .Dimnames = list(c("1", 
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12"), c("Neutrophil", 
"Tcell", "Monocyte", "Bcell", "NKcell", "PlasmaCell", "DendriticCell"
)))

并用这段代码

par(mfrow=c(2,3), mai=c(1,0.4,0.4,0.1), omi=rep(0,4))
    for ( i in c(2:7)){
        # deliberately skip i=1
        # so we 2 x 3 can fit in image

        boxplot(SPVsR_i[,i]~as.factor(samples_i), outline=F, density=c(10,20,300),  las=2, yaxt="n", col=c(brewer.pal(3,"Blues"),
        brewer.pal(3, "Oranges")), density=c(10,20,300), at=c(1,2,3,5,6,7))
        title(colnames(irisTag_i)[i])
    }

我可以制作这张图片：

使用上面相同的三个数据帧，如何使用ggplot2产生相似的结果？

我尝试了这个但是失败了：

library(reshape2)
library(ggplot2)

nsamplesv <- cbind(SPVsR_i, samples_i,deparse.level=2)
nsamplesv_df <- as.data.frame.matrix(nsamplesv)
nsamplesv.m <- melt(nsamplesv_df,id.vars=c('samples_i'))
colnames(nsamplesv.m) <- c("samples",'celltype','score')

p <- ggplot(nsamplesv.m, aes(samples,score)) +geom_boxplot() +facet_wrap( ~ celltype)
p

产生此图像：

我不知道具体如何：

• 用更少的刻度和3个小数位固定y轴。
• 框不显示。 每个框架应有6个盒子。
• 想给盒子上色。 LAIV为蓝色，TIV为黄色的那些。
• 将x轴旋转180度。

Answer 1

这是重塑数据的更好方法：

library(ggplot2)
library(dplyr)
library(tidyr)
library(RColorBrewer)

as_data_frame(SPVsR_i) %>% 
  bind_cols(data_frame(sample=samples_i)) %>% 
  gather(celltype, score, -sample) %>% 
  mutate(celltype=factor(celltype, levels=unique(celltype))) %>% 
  filter(!(celltype %in% c("Neutrophil"))) -> df

ggplot2需要将美感映射到数据帧，或确保引用的变量与您使用的数据具有相同的长度。

我在这里模仿了您想要的输出，但是请考虑尊重您的观看者，而不是让他们的头倾斜以阅读X轴标签。 箱线图确实还应该具有（IMO）主Y轴线，因此人脑更容易解码这些值。 这不是100％必要的，但（再次）重点是帮助理解。

您也没有注意到绘图中的免费Y轴刻度，我不在这里，但这也有点令人恐惧。 即使使用Y轴刻度标签，您也应该做一些事情以确保人们不会试图比较比例完全相同的细胞类型（他们在解码图时会默认/自动进行比较，但是会额外加标签）如果人们阅读了上述指南，将会强制执行额外的处理步骤）。

p <- ggplot(df, aes(sample, score))
p <- p + geom_boxplot(aes(fill=sample))
p <- p + scale_fill_manual(values=c(brewer.pal(3,"Blues"), brewer.pal(3,"Oranges")))
p <- p + facet_wrap(~celltype, scales="free")
p <- p + labs(x=NULL, y=NULL)
p <- p + theme_bw(base_size=10)
p <- p + theme(strip.background=element_blank())
p <- p + theme(strip.text=element_text(face="bold"))
p <- p + theme(axis.text.x=element_text(angle=90, vjust=0.5))
p <- p + theme(panel.grid.major.x=element_blank())
p <- p + theme(panel.grid.major.y=element_blank())
p <- p + theme(panel.grid.minor.y=element_blank())
p <- p + theme(panel.margin=margin(20,20,20,20))
p <- p + theme(plot.margin=margin(20,20,20,20))
p <- p + theme(legend.position="none")
p