some weird arrow head being generated.

[mdagit]

Below is my R program, then the input data, and attached is the svg string and the visual rendering.
You can see in the bottom right a weird distorted arrowhead polygon.
I tried both the latest release and latest main branch.

library(consort)
library(DiagrammeRsvg)

df <- read.csv(file("stdin"))

out <- consort_plot(data = df,
order = c(trialno = "Assessed for Eligibility",
exc = "Excluded",
arm = "Randomized",
fow1 = "Never Started",
trialno = "Follow Up",
fow2 = "Discontinued",
trialno = "Final Analysis"),
side_box = c("exc", "fow1", "fow2"),
allocation = "arm",
labels = c("1" = "Enrollment", "2" = "Allocation",
"4" = "Follow-Up",
"5" = "Final Analysis"),
cex = 0.6)

svg <- export_svg(plot(out, grViz = TRUE))

library(htmltools)
print(HTML(svg))

---

trialno,exc,arm,fow1,fow2
1,NA,Yoga Standard,NA,NA
2,NA,Yoga Ayurvedic,NA,NA
3,NA,Education Control,NA,NA
10,Substance Misuse,NA,NA,NA
11,Currently Practicing Yoga,NA,NA,NA
20,NA,Yoga Standard,reason unknown,NA
21,NA,Yoga Ayurvedic,work/school/childcare conflict,NA
30,NA,Education Control,NA,injury outside study
31,NA,Yoga Ayurvedic,NA,work conflict

[adayim]

Hi, sorry for the late response. But I think the output is correct from what I see it. The below is the code I used to plot.

plot(out, grViz = TRUE)

It seems like you want to export the figure to svg. You can find example here. You can use the code below:

plot(out, grViz = TRUE) |> 
  DiagrammeRsvg::export_svg() |> 
  charToRaw() |> 
  rsvg::rsvg_svg("svg_graph.svg")

Check out the helpfile of the rsvg package for other formats.

[mdagit]

wow it is kind of surprising to me that just that small change results in unmangled output.
in my case i need the svg (xml) output sent to stdout (not a named file).
I know this seems super-basic, but how is that done?
Thanks a bunch.

[adayim]

I am not sure if I understand you question but the SVG is an XML file. I am guessing you want to embed it in the HTML file? You can use xml2 package to read the SVG file or the following to produce an HTML file:

grviz_txt <- build_grviz(out)
DiagrammeR::grViz(grviz_txt)

[mdagit]

Well, my R skills are quite limited but I couldn't find a decent CONSORT utility except in R.
I was just trying to get my R script to print to stdout console instead of to a file.
In the end I took your code and added a cat:

plot(out, grViz = TRUE) |> 
  DiagrammeRsvg::export_svg() |> 
  charToRaw() |> 
  rsvg::rsvg_svg("svg_graph.svg")
  
  system("cat svg_graph.svg");

But now I have a new problem (and I have no idea why this is happening), but the text no longer fits in the boxes:


[adayim]

Do you think I am correct that you want an SVG file? To get an SVG output, could you just use the following?

plot(out, grViz = TRUE) |> 
  DiagrammeRsvg::export_svg() |> 
  charToRaw() |> 
  rsvg::rsvg_svg("svg_graph.svg")

You can also get other formats than the SVG.

Or use the following to get a Graphviz file and render it with other packages that you are familiar with?

grviz_txt <- build_grviz(out)
cat(grviz_txt , file = "consort.gv")

[mdagit]

i don't want an intermediary file in the file system -- i want the xml sent to stdout (console) so that it can then be piped into other processing. This is being invoked as a subprocess using RScript. I would prefer to not have an intermediary file because then I will have temp files to clean up, or a potential race condition if the process is run concurrently with the same file name. Thanks. I think my problems are partly due to being a newbie at R, and partly because there is some issue with setting drawing bounds (my guess).

…

On Fri, Dec 6, 2024, at 1:09 AM, Alim Dayim wrote: Do you think I am correct that you want an SVG file? To get an SVG output, could you just use the following? plot(out, grViz = TRUE) |> DiagrammeRsvg::export_svg() |> charToRaw() |> rsvg::rsvg_svg("svg_graph.svg") You can also get other formats than the SVG. Or use the following to get a Graphviz file and render it with other packages that you are familiar with? grviz_txt <- build_grviz(out) cat(grviz_txt , file = "consort.gv") — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQZW6QQQR3JVKCHYKY7GKT2EFST5AVCNFSM6AAAAABRYE4K2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMRSGU4TGNJRGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>