如何使用ggplot2创建刻面的箱形图

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"
)))

使用此代码

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框，我如何使用ggplot2产生类似的结果？

我尝试了但失败了：

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

制作此图片：

我不知道如何：

• 固定y轴，使用更少的刻度和3位小数。
• 盒子不会出现。每个框架应该有6个框。
• 想为盒子上色。 LAIV为蓝调，TIV为黄色的。
• 将x轴旋转180度。

Answer 1

以下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要求将美学映射到数据框或确保引用的变量与您使用的数据长度相同。

我已经在这里模仿了您想要的输出，但请考虑尊重您的观众，而不是让他们倾斜头来阅读X轴标签。箱形图实际上也应该具有（IMO）主要的Y轴线，因此人类大脑更容易解码这些值。它不是100％必要的，但（再次）重点是帮助理解。

你也没有注意到你的情节中的自由Y轴刻度，我不会在这里，但这也有点像horribad。即使使用Y轴刻度标签，您也应该采取措施确保人们不会尝试使用完全相同的刻度比较各种类型（默认情况下/他们会自动解码绘图但额外的标签将强制执行额外的处理步骤，前提是人们阅读了上述指南。

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