使用R制作流程图

Question

使用R制作流程图

4

我一整天都在努力创建一个流程图，代表我们在研究中所包含的某些患者。

我已经在Power Point演示文稿中准备好了一个草稿版本，描绘了我正在寻找的排列方式。

现在，我已经准备好了所有的框，但是我需要与附图中相同的箭头对齐和连接。我尝试复制并粘贴了这个页面上的指南https://cran.r-project.org/web/packages/Gmisc/vignettes/Grid-based_flowcharts.html，但是现在我卡住了。由于我在使用R方面的专业知识很少，只有偶尔使用它，你可能会看到一些容易的东西，我却看不到。

这是我的代码：

  install.packages("Gmisc")
library(Gmisc, quietly = TRUE)
library(glue)
library(htmlTable)
library(grid)
library(magrittr)

org_cohort <- boxGrob(glue("Patients with pancreatic cancer admitted to the University Clinic of Essen",
                           "from 01/2002 to 08/2020",
                           "n = {pop}",
                           pop = txtInt(909),
                           .sep = "\n"))
included <- boxGrob(glue("Patients with genetic sequencing and survival data",
                         "n = {incl}",
                         incl = txtInt(412),
                         .sep = "\n"))
grp_a <- boxGrob(glue("Patients treated with FOLFIRINOX or Gemcitabine / nab-Paclitaxel",
                      "n = {recr}",
                      recr = txtInt(179),
                      .sep = "\n"))

grp_b <- boxGrob(glue("Patients with genetic sequencing data via MAPK-TRON panel",
                      "n = {recr}",
                      recr = txtInt(185),
                      .sep = "\n"))

excluded_1 <- boxGrob(glue("Excluded (n = {tot}):",
                         " - No survival data: {NoSurv}",
                         " - No MAPK-Tron panel and early available abdominal CT-scan: {NoMAPKCT}",
                         tot = 506,
                         NoSurv = 300,
                         NoMAPKCT = 206,
                         .sep = "\n"),
                    just = "left")

excluded_2 <- boxGrob(glue("Excluded (n = {NoFGP}):",
                           " - No FOLFIRINOX or Gemcitabine / nab-Paclitaxel as 1st line: {NoFGP}",
                           NoFGP = 233,
                           .sep = "\n"),
                      just = "left")

excluded_3 <- boxGrob(glue("Excluded (n = {NoMAPK}):",
                           " - No sequencing data available: {NoMAPK}",
                           NoMAPK = 227,
                           .sep = "\n"),
                      just = "left")

grid.newpage()
vert <- spreadVertical(org_cohort = org_cohort,
                       included = included,
                       grps = grp_a)
grps <- alignVertical(reference = vert$grp_a,
                      grp_a, grp_b) %>%
  spreadHorizontal()
vert$grps <- NULL

excluded_1 <- moveBox(excluded_1,
                    x = .8,
                    y = coords(vert$included)$top + distance(vert$included, vert$org_cohort, half = TRUE, center = FALSE))

excluded_2 <- moveBox(excluded_2,
                      x = .8,
                      y = coords(vert$grp_a)$top + distance(vert$included, vert$grp_a, half = TRUE, center = FALSE))

excluded_3 <- moveBox(excluded_3,
                      x = .8,
                      y = coords(vert$grp_b)$bottom + distance(vert$included, vert$grp_b, half = TRUE, center = FALSE))

## already facing problems here: R gives me the following error message: Error in coords(vert$grp_a/b) : 
  #Assertion on 'box' failed: Must inherit from class 'box', but has class 'NULL'..

for (i in 1:(length(vert) - 1)) {
  connectGrob(vert[[i]], vert[[i + 1]], type = "vert") %>%
    print
}
connectGrob(vert$included, grps[[1]], type = "N")
connectGrob(vert$included, grps[[2]], type = "N")

connectGrob(vert$included, excluded_1, type = "L")
connectGrob(vert$grp_a, excluded_2, type = "L")



# Print boxes
vert
grps
excluded_1
excluded_2
excluded_3

我会坦诚地说：在 "grid.newpage()" 之后的代码我不太理解。因此，我一直在尝试理解代码组件实际执行的操作，但每次我认为我已经理解了它的工作原理时，又会有另一个挫折等着我。

R基本上给我一个箭头和盒子到处都是的图表，但并不是我想要的样子。然后有时我的盒子甚至太大或什么的？特别是图表末尾的两个子组的盒子经常被切断...

你有没有想法如何“强制”R为我复制那种图表（见图片）？

非常感谢您的帮助，这将使我更接近最终完成论文...！

提前致谢！

- Pharmacos

1

我可能会考虑使用 DiagrammeR 包来完成这样的任务：https://datascienceplus.com/how-to-build-a-simple-flowchart-with-r-diagrammer-package/ - Ben

@Ben 谢谢，这看起来肯定更容易...我稍后会试一下！ - Pharmacos

好的，DiagrammeR似乎没有一个函数可以同时在垂直和水平方向上连接两个其他框与一个框...也许我漏掉了什么，但我没有找到任何关于如何使用这个包来实现它的线索。 - Pharmacos

1个回答

网页内容由stack overflow 提供, 点击上面的

可以查看英文原文，
原文链接

- Ben · Accepted Answer

以下是关于 DiagrammeR 的一些入门内容。

使用 splines = ortho 可以获得 90 度角和直线。
在节点标签中使用 <br/> 添加换行。
使用空白节点来获得排除框的分支。然后使用 rank 将隐藏的空白节点与排除框对齐。

希望这对你有所帮助。

library(DiagrammeR)

grViz(
     "digraph my_flowchart { 
      graph[splines = ortho]
      node [fontname = Helvetica, shape = box, width = 4, height = 1]
      
        node1[label = <Pancreatic cancer patients treated at our center<br/>diagnosed 2002-2020<br/>(n = 909)>]
        node2[label = <Patients with MAPK-TRON panel and/or<br/>early available abdominal CT scan (n = 412)>]
        
        blank1[label = '', width = 0.01, height = 0.01]
        excluded1[label = <Exclusion of patients without<br/>(1) MARK-TRON panel and early available abdominal CT scan, and<br/>(2) survival data<br/>(n = 506)>]
        
        node1 -> blank1[dir = none];
        blank1 -> excluded1[minlen = 2];
        blank1 -> node2;
        { rank = same; blank1 excluded1 }
        
        node3[label = <FOLFIRINOX or Gemcitabine/nab-Paclitaxel as first CTx<br/>(n = 179)>]
        node4[label = <Patients with MAPK-TRON panel regardless of CT scans<br/>(n = 185)>]
        
        blank2[label = '', width = 0.01, height = 0.01]
        excluded2[label = <Exclusion of patients that did not receive<br/>FOLFIRINOX or Gemcitabine/nab Paclitaxel as first CTx<br/>(n = 233)>]
        
        blank3[label = '', width = 0.01, height = 0.01]
        excluded3[label = <Exclusion of patients without MAPK-TRON panel<br/>(n = 227)>]
        
        node2 -> blank2[dir = none];
        node2 -> blank3[dir = none];
        
        blank2 -> excluded2[minlen = 2];
        blank3 -> excluded3[minlen = 2];
        
        blank2 -> node3;
        blank3 -> node4;
        
        { rank = same; blank2 excluded2 blank3 excluded3 }
     }"
)

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