TraMineR与seqHMM绘图布局异常：如何单页展示4幅图

问题背景 #

使用TraMineR绘制2幅序列分布图（seqplot(type='d')），并在下方对应绘制2个隐马尔可夫模型（HMM）图，通过layout()设置2行2列布局后，前3幅图能正常显示，但第4幅HMM图会跳转到新页面，导致右下角区域留白。

可复现代码：

library('seqHMM')
library('TraMineR')

data("biofam")
biofam <- biofam[sample(nrow(biofam),300),]
biofam.lab <- c("Parent", "Left", "Married", "Left+Marr",
                "Child", "Left+Child", "Left+Marr+Child", "Divorced")
biofam.seq <- seqdef(biofam, 10:25, labels=biofam.lab)

### Fit a Hidden Markov Model
biofam.hmm <- build_hmm(observations = biofam.seq, n_states = 3)

### 尝试布局绘图
layout(matrix(c(1,2,3,4), ncol = 2, byrow = TRUE))
layout.show(4)

par(cex = 0.65, mar = c(2.5,4.1,2.5,1.5))
### 序列分布图
seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)
seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)

### HMM图
par(cex = 0.5, mar = c(1.5,3.5,3.5,1.5))
plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)
plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)

问题原因 #

TraMineR的seqplot基于基础绘图系统，而seqHMM的plot.bhmm方法（绘制HMM）基于grid绘图系统，两个系统的布局管理不兼容。layout()仅对基础绘图系统生效，当绘制第一个HMM图时，grid系统会重置绘图设备，导致后续的HMM图无法进入预设的layout区域。

解决方法 #

方法1：用gridBase协调双绘图系统 #

使用gridBase包让HMM图正确嵌入layout指定的区域，具体代码如下：

library('seqHMM')
library('TraMineR')
library(grid)
library(gridBase)

data("biofam")
biofam <- biofam[sample(nrow(biofam),300),]
biofam.lab <- c("Parent", "Left", "Married", "Left+Marr",
                "Child", "Left+Child", "Left+Marr+Child", "Divorced")
biofam.seq <- seqdef(biofam, 10:25, labels=biofam.lab)

biofam.hmm <- build_hmm(observations = biofam.seq, n_states = 3)

### 设置2行2列布局
layout(matrix(c(1,2,3,4), ncol = 2, byrow = TRUE))

# 绘制第一幅序列图
par(cex = 0.65, mar = c(2.5,4.1,2.5,1.5))
seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)

# 绘制第二幅序列图
seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)

# 绘制第一幅HMM图
par(cex = 0.5, mar = c(1.5,3.5,3.5,1.5))
grid.newpage()
vps <- baseViewports()
pushViewport(vps$inner, vps$figure, vps$plot)
plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)
popViewport(3)

# 绘制第二幅HMM图
grid.newpage()
vps <- baseViewports()
pushViewport(vps$inner, vps$figure, vps$plot)
plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)
popViewport(3)

方法2：用gridExtra统一转为grid对象布局 #

将所有图转换为grid对象，通过gridExtra::grid.arrange()统一管理布局：

library('seqHMM')
library('TraMineR')
library(grid)
library(gridExtra)
library(gridGraphics)

data("biofam")
biofam <- biofam[sample(nrow(biofam),300),]
biofam.lab <- c("Parent", "Left", "Married", "Left+Marr",
                "Child", "Left+Child", "Left+Marr+Child", "Divorced")
biofam.seq <- seqdef(biofam, 10:25, labels=biofam.lab)

biofam.hmm <- build_hmm(observations = biofam.seq, n_states = 3)

# 将序列图转为grid对象
seq1 <- grid.grabExpr({
  par(cex = 0.65, mar = c(2.5,4.1,2.5,1.5))
  seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)
})

seq2 <- grid.grabExpr({
  par(cex = 0.65, mar = c(2.5,4.1,2.5,1.5))
  seqplot(biofam.seq, type = 'd', with.legend = FALSE, border = NA, ylab = NA)
})

# 将HMM图转为grid对象
hmm1 <- grid.grabExpr({
  plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)
})

hmm2 <- grid.grabExpr({
  plot(biofam.hmm, with.legend = FALSE, vertex.size = 15)
})

# 2行2列布局
grid.arrange(seq1, seq2, hmm1, hmm2, ncol=2)

内容的提问来源于stack exchange，提问作者BossVom Schloss