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Flow charts in R

May 9, 2018

Flow charts are an important part of a clinical trial report. Making them can be a pain though. One good way to do it seems to be with the grid and Gmisc packages in R. X and Y coordinates can be designated based on the center of the boxes in normalized device coordinates (proportions of the device space – 0.5 is this middle) which saves a lot of messing around with corners of boxes and arrows.

A very basic flow chart, based very roughly on the CONSORT version, can be generated as follows…

library(grid)
library(Gmisc)

grid.newpage()
# set some parameters to use repeatedly
leftx <- .25
midx <- .5
rightx <- .75
width <- .4
gp <- gpar(fill = "lightgrey")
# create boxes
(total <- boxGrob("Total\n N = NNN", 
 x=midx, y=.9, box_gp = gp, width = width))

(rando <- boxGrob("Randomized\n N = NNN", 
 x=midx, y=.75, box_gp = gp, width = width))
# connect boxes like this
connectGrob(total, rando, "v")

(inel <- boxGrob("Ineligible\n N = NNN", 
 x=rightx, y=.825, box_gp = gp, width = .25, height = .05))

connectGrob(total, inel, "-")

(g1 <- boxGrob("Allocated to Group 1\n N = NNN", 
 x=leftx, y=.5, box_gp = gp, width = width))
(g2 <- boxGrob("Allocated to Group 2\n N = NNN", 
 x=rightx, y=.5, box_gp = gp, width = width))

connectGrob(rando, g1, "N")
connectGrob(rando, g2, "N")

(g11 <- boxGrob("Followed up\n N = NNN", 
 x=leftx, y=.3, box_gp = gp, width = width))
(g21 <- boxGrob("Followed up\n N = NNN", 
 x=rightx, y=.3, box_gp = gp, width = width))

connectGrob(g1, g11, "N")
connectGrob(g2, g21, "N")

(g12 <- boxGrob("Completed\n N = NNN", 
 x=leftx, y=.1, box_gp = gp, width = width))
(g22 <- boxGrob("Completed\n N = NNN", 
 x=rightx, y=.1, box_gp = gp, width = width))

connectGrob(g11, g12, "N")
connectGrob(g21, g22, "N")

Sections of code to make the boxes are wrapped in brackets to print them immediately. The code creates something like the following figure:

flowtemp

For detailed info, see the Gmisc vignette. This code is also on github.

 

 

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From → R, Uncategorized

7 Comments
  1. RAB permalink

    is it possible to save the output of this to a pdf or png? I am trying to use this within a function and would like to automatically save, but I can’t figure out how.

    • it should just be a case of opening the relevant device before creating the flow chart and closing it afterwards…

      png(“filename.png”)
      # code for plot here
      dev.off()

      • RAB permalink

        Awesome, thanks, works like a charm. One small problem though, in pdf the horizontal arrow no longer aligns with the ineligible boxGrob in pdf form. Instead it goes somewhere in the middle of the box. Is there a way to force the arrow to touch the edge no matter the width of the pdf page?

      • You solved this as I understand…
        For others… see the issue here: https://github.com/aghaynes/misc/issues/1

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