如何在R corrgram中具有轴标签? [英] How to have axis labels in R corrgram?

问题描述

我想在x轴和y轴上有水平和垂直标签，请参见以下伪代码. Henrik对相关主题2013的评论是关于关闭对角标签，然后尝试为轴关联标签，但是我不想关闭对角标签

I would like to have horizontal and vertical labels on x-axis and y-axis, see the following pseudocode. Henrik's comment of the related thread 2013 is about turning off diagonal labels and then trying to associate labels for the axes, but I do not want to turn off the diagonal labels

您可以通过将标签设置为NULL来关闭对角标签.然后，您可以尝试通过使用文本在您想要的位置添加标签

You may turn the diagonal labels off by setting labels = NULL. Then you can try to add your labels where you wish by using text

library("corrgram")
ids <- c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18)
# https://cran.r-project.org/web/packages/corrgram/vignettes/corrgram_examples.html
corrgram(baseball,main="Baseball data PC2/PC1 order") +
          xlab("Patient 1 ID") +
          ylab("Patient 2 ID") +
          scale_x_discrete(labels = ids) +
          scale_y_discrete(labels = ids)

图. 1个测试数据

最好在第一个参数位置重载所有可能的参数，然后在新函数中仅包含一个额外的参数ids；伪代码

It would be nice to overload the first parameter place with all possible parameters and then have only one extra paremeter ids in the new function; pseudocode

# https://stackoverflow.com/a/40387233/54964
corrgramLabels <- function(x, ids){
        corrgram(x=x)
        mtext("Patient 1 ID", side = 1, line = 4)
        mtext("Patient 2 ID", side = 2, line = 3)
        x_at <- seq(0.075, 0.925, length.out = length(ids))
        y_at <- seq(0.075, 0.91, length.out = length(ids))
        axis(1, at=x_at, labels=x_labels, line = 1.5, tick=F, cex.axis=.7)
        axis(2, at=y_at, labels=y_labels, line = 1, tick=F, cex.axis=.7)
}

尝试使用它，但出现以下错误

Attempt to use it but the following error

corrgramLabels(M,
  upper.panel=panel.pie,
  lower.panel=panel.shade,
  text.panel=panel.txt,
  order=NULL,
  diag.panel=panel.minmax,
  main=title)

错误

Error in corrgramLabels(M, upper.panel = panel.pie, lower.panel = panel.shade,  : 
  unused arguments (upper.panel = panel.pie, lower.panel = panel.shade, text.panel = panel.txt, order = NULL, diag.panel = panel.minmax, main = title)
Execution halted

解决方案的建议

我实际上认为最好的解决方案是独立于corrgram的功能.在corrgram()之后启动功能createLabels()，您会得到结果.有可能吗?

Proposal for the solution

I actually think that the best solution would be a function independent of corrgram. Start a function createLabels() after corrgram() and you get the result. Is that possible?

操作系统:Debian 8.5
R:3.3.1
相关: Corrgram包水平和垂直标签

OS: Debian 8.5
R: 3.3.1
Related: Corrgram Package Horizontal and Vertical Labels

推荐答案

对于轴，您可以使用mtext(m用于边距区域；文本将不起作用):

For the axes you can use mtext (m for margin region; text will not work):

library("corrgram")
ids <- seq(1, 18)
corrgram(baseball,main="Baseball data PC2/PC1 order")

mtext("Patient 1 ID", side = 1, line = 4)
mtext("Patient 2 ID", side = 2, line = 3)

您可以使用line参数来增加或减少到实际绘图的距离.

You can use the line parameter to increase or decrease the distance to the actual plot.

标签比较困难.您可以使用mtext或axis来完成此操作，但是如果您调整图形的大小，那么它将不适合其余的图形.因此，这并不是最佳选择.如果您知道自己的身材将是多少，它应该仍然有效.例如800x800像素，请优化位置(在参数处):

The labels are more difficult. You could do it with mtext or axis, but if you resize the figure, it won't fit with the rest. So this is not really optimal. If you know how large your figure will be, it should still work; for example 800x800 pixels, optimize the position (at parameter):

axis(1, at=seq(0.09, 0.91, length.out = length(ids)),
     labels=as.character(ids), line = 1.5, tick=F, cex.axis=.7)
axis(2, at=seq(0.08, 0.88, length.out = length(ids)),
     labels=as.character(ids), line = 1, tick=F, cex.axis=.7)

图输出: 使用轴和标签测试数据

为获得更好的解决方案，您可能需要查看函数内部，并找出框的绘制方式和确切位置.

For a better solution, you might need to look inside the function and find out how and where exactly the boxes are drawn.

在Masi评论后 当然，我们可以围绕它构建一个函数:

Edit after comment by Masi: Of course we can build a function around that:

corrgramMasi <- function(x, main, xlab, ylab, x_labels, y_labels, x_at, y_at){
  corrgram(x=x, main=main)
  mtext(xlab, side = 1, line = 4)
  mtext(ylab, side = 2, line = 3)
  axis(1, at=x_at, labels=x_labels, line = 1.5, tick=F, cex.axis=.7)
  axis(2, at=y_at, labels=y_labels, line = 1, tick=F, cex.axis=.7)
}

使用具有调整后的"at"参数值的功能来保存分辨率为800x800像素的图形的说明:

Illustration to use the function with adjusted "at" parameter values to save the figure with a resolution of 800x800 pixels:

x_at <- seq(0.075, 0.925, length.out = length(ids))
y_at <- seq(0.075, 0.91, length.out = length(ids))
png("corrgramMasi.png", width=800, height=800)
  corrgramMasi(baseball, "Baseball data PC2/PC1 order", xlab="Patient 1 ID",
               ylab="Patient 2 ID", x_labels=ids, y_labels=ids, x_at=x_at, y_at=y_at)
dev.off()

如果您有多个Corrgram，则可以仅使用Map并专门更改参数.在这种情况下，我只需使用两次棒球数据集并更改标题，但将所有其他变量保持不变:

And if you have several corrgrams, you could just use Map and change parameters specifically. In this case I simply use the baseball data set two times and change the title, but leave all other variables constant:

Map(corrgramMasi, x=list(baseball, baseball), main=list("title 1", "title 2"), 
    xlab="Patient 1 ID", ylab="Patient 2 ID", x_labels=ids, y_labels=ids,
    x_at=x_at, y_at=y_at)

如果您有10个Corrgrams，则只需将数据放入x列表中并更改标题(或将它们也设置为恒定值).如果您要更改其他值(例如xlab)，则必须使用带有相应值的列表，例如xlab = list("Corrgram 1的xlab"，"Corrgram 2的xlab"，...).

If you have 10 corrgrams, then just put the data into the x list and change the titles (or set them to a constant value as well). If you want to change another value (e.g. xlab) you will have to use a list with the corresponding values, e.g. xlab=list("xlab for corrgram 1", "xlab for corrgram 2", ...).

但是如前所述，"at"参数在这里有点脏，因此这当然不是最佳解决方案.

But as said earlier, the "at" parameter is kind of dirty here, so this is certainly not the best solution.

如Masi所建议，最好使用单独的函数来创建标签:

Edit 2: As suggested by Masi it is probably better to use a separate function for creating the labels:

createLabels <- function(xlab, ylab, x_labels, y_labels, x_at, y_at){
  mtext(xlab, side = 1, line = 4)
  mtext(ylab, side = 2, line = 3)
  axis(1, at=x_at, labels=x_labels, line = 1.5, tick=F, cex.axis=.7)
  axis(2, at=y_at, labels=y_labels, line = 1, tick=F, cex.axis=.7)
}

然后在制作Corrgram后调用createLabels:

Then call createLabels after making the corrgram:

corrgram(baseball,main="Baseball data PC2/PC1 order")
createLabels(xlab="Patient 1 ID", ylab="Patient 2 ID", x_labels=ids,
             y_labels=ids, x_at=x_at, y_at=y_at)

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