How to save a flowchart made with grid and Gmisc

Question

What I want to do is to create a basic flowchart with R, add it to my R Markdown file and make it referencable (if possible like I did with my ggplot2 figures -> fig.cap = " " in the code chunk header).

The Flowchart:

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
(Pharmazie <- boxGrob("Verbrauchsdaten von der\n Spitalpharmazie (Excel-Tabelle)", 
                  x=leftx, y=0.876, box_gp = gp, width = width))

(Finanzen <- boxGrob("Belegzahlen vom Ressort\n Finanzen (Excel-Tabelle)", 
                 x=rightx, y=.876, box_gp = gp, width = width))

(A <- boxGrob("Import der Daten aus Excel ins\n Microsoft Access (Datenbanksoftware)", 
          x=midx, y=0.76, box_gp = gp, width = width))

(B <- boxGrob("Zusammenführen der Informationen\n und erstellen neuer, berechneter Tabellen", 
          x=midx, y=.64, box_gp = gp, width = width))

(C <- boxGrob("Export der neu erstellten Tabellen\n in Form von Excel-Tabellen", 
          x=midx, y=.52, box_gp = gp, width = width))

(D <- boxGrob("Import der neuen Tabellen in R", 
          x=midx, y=.414, box_gp = gp, width = width))

(E <- boxGrob("Berechnung und grafische Darstellung\n der Grafiken und Tabellen", 
          x=midx, y=.308, box_gp = gp, width = width))


connectGrob(Pharmazie, A, "L")
connectGrob(Finanzen, A, "L")
connectGrob(A, B, "N")
connectGrob(B, C, "N")
connectGrob(C, D, "N")
connectGrob(D, E, "N")

The problem that I'm having is that I cannot find a way to save the flowchart to a variable / png file (to import it into my R Markdown file later) or, even better, to include it directly within a code chunk (it looks different when I execute the code within a code chunk vs. when executing it in a script, also when trying to give it a fig.cap it fails to knit).

Example of how differently it looks: .

Any help would be greatly appreciated!

P.S. I tried to make the flowchart with the package "DiagrammeR", but I gave up after I did not manage to find a way to have the text on more than one line per box (so it wouldn't be so broad).

Answer 1

For reference png() is how you would easily save your flowchart to a png file. Other formats are possible, like pdf(). Below is how you would save the vignette example to a png file, though you won't see it in the viewport as you run the code. Note dev.off() at the end.

#r flowchart with gmisc
#https://cran.r-project.org/web/packages/Gmisc/vignettes/Grid-based_flowcharts.html

#install.packages("Gmisc")
library(Gmisc)
library(grid)
#example x

#get file ready to receive image
png("vignette flowchart.png", width=500, height = 500, units = "px")

grid.newpage()

# Initiate the boxes that we want to connect
side <- boxPropGrob("Side", "Left", "Right", 
                    prop=.3, 
                    x=0, y=.9,
                    bjust = c(0,1))

start <- boxGrob("Top", 
                 x=.6, y=coords(side)$y, 
                 box_gp = gpar(fill = "yellow"))

bottom <- boxGrob("Bottom", x=.6, y=0, 
                  bjust="bottom")


sub_side_left <- boxGrob("Left", 
                         x = coords(side)$left_x, 
                         y = 0,
                         bjust = "bottom")
sub_side_right <- boxGrob("Right", 
                          x = coords(side)$right_x, 
                          y = 0,
                          bjust = "bottom")

odd <- boxGrob("Odd\nbox", 
               x=coords(side)$right, 
               y=.5)

odd2 <- boxGrob("Also odd", 
                x=coords(odd)$right + 
                  distance(bottom, odd, type="h", half=TRUE) -
                  unit(2, "mm"), 
                y=0,
                bjust = c(1,0))

exclude <- boxGrob("Exclude:\n - Too sick\n - Prev. surgery", 
                   x=1, y=coords(bottom)$top + 
                     distance(start, bottom, 
                              type="v", half=TRUE), 
                   just="left", bjust = "right")

# Connect the boxes and print/plot them



connectGrob(start, bottom, "vertical")
connectGrob(start, side, "horizontal")
connectGrob(bottom, odd, "Z", "l")
connectGrob(odd, odd2, "N", "l")
connectGrob(side, sub_side_left, "v", "l")
connectGrob(side, sub_side_right, "v", "r")
connectGrob(start, exclude, "-", 
            lty_gp = gpar(lwd=2, col="darkred", fill="darkred"))

# Print the grobs
start
bottom
side
exclude
sub_side_left
sub_side_right
odd
odd2

#save and close file
dev.off()

Answer 2

It looks different, because the viewport you are drawing on is not the same. You just need to fiddle a bit with the positioning options to make it fit. Below I used fig.width and fig.height and created a wrapper function in which I also vertically justified the boxes (top end). This makes it easier to build the chart top to bottom using the y coordinate.

---
output: pdf_document
---


```{r echo = F, message = F, fig.width=7, fig.height = 6}
library(grid)
library(Gmisc)

# grid.newpage()
# set some parameters to use repeatedly
leftx <- .2
midx <- .5
rightx <- .8

myBoxGrob <- function(text, ...) {
  boxGrob(label = text, bjust = "top", box_gp = gpar(fill = "lightgrey"), ...)
}

# create boxes
(Pharmazie <- myBoxGrob("Verbrauchsdaten von der\n Spitalpharmazie (Excel-Tabelle)", x=leftx, y=1, width = 0.38))
(Finanzen <- myBoxGrob("Belegzahlen vom Ressort\n Finanzen (Excel-Tabelle)", x=rightx, y=1, width = 0.38))
(A <- myBoxGrob("Import der Daten aus Excel ins\n Microsoft Access (Datenbanksoftware)", x=midx, y=0.87, width = 0.5))
(B <- myBoxGrob("Zusammenführen der Informationen\n und erstellen neuer, berechneter Tabellen", x=midx, y=.70, width = 0.5))
(C <- myBoxGrob("Export der neu erstellten Tabellen\n in Form von Excel-Tabellen", x=midx, y=.53, width = 0.5))
(D <- myBoxGrob("Import der neuen Tabellen in R", x=midx, y=.36,  width = 0.5))
(E <- myBoxGrob("Berechnung und grafische Darstellung\n der Grafiken und Tabellen", x=midx, y=.21, width = 0.5))


connectGrob(Pharmazie, A, "L")
connectGrob(Finanzen, A, "L")
connectGrob(A, B, "N")
connectGrob(B, C, "N")
connectGrob(C, D, "N")
connectGrob(D, E, "N")
```

If the flowchart is acceptable, you can scale the plot using the chunk option out.width (here =".5\\textwidth"):