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Venndir Book

13jul2025

  • Add examples for adding fonts: systemfonts: `systemfonts::get_from_google_fonts("familyname")

  • Document any unexpected dependencies for building the Venndir book

    • Fonts: Bradley Hand: "Shadows Into Light" Optima: "Commissioner" Futura: "Play" Chalkduster: "Bubblegum Sans" La Parisienne Script: "Parisienne" Proxima Nova: "Monda"
    • Consider encoding alternative fonts upfront, hidden R code? Or converting each to a Google Font?

10jul2025 To Consider

  • About the cover image - Christina Ward
  • Change "What is a Venn Diagram?" to "What is a Venndir Diagram?"?
  • Add "How to Cite This Book"
@book{wardvenndir2025,
  title={Venndir},
  author={Ward, James M},
  year={2025},
  publisher={Ward},
  url={https://jmw86069.github.com/venndir-book}
}
  • Clean up the cover image presentation in each format.
  • Short biorxiv paper to cite for Venndir.
  • How to install Venndir.

Debug Rendering Crash

Section [advanced-signs-1c] rendering custom Unicode symbols by marquee.

  • Restart RStudio before rendering (Ctrl-Shift-F10).
  • Use "Arial" or "Times"
  • Try rendering in R console, not within RStudio.
  • Try previewing the chapter: bookdown::preview_chapter("04-customizations.Rmd", output_format="epub_book")

Todo from C's Edits

  • Intro - be bold, describe the value. Add more
  • Chapter 1
    • Expand the description of the Venn diagram. E.g. set A has (5 + 2) = 7 items total. Set B has (3 + 2) = 5 items total.
    • Add description of directional Venn.
    • Consider expanding to include a description of the Venndir legend.

Short list

  • Add "When and How to Use a Venn Diagram"

Add Definitions / Conventions

  • Describe how to use expand_fraction

  • R code examples are shown in mono-spaced text, with light gray background

  • Output from an R command is shown as mono-spaced text with a prefix '#'.

  • set

  • vector

  • signed data

  • incidence matrix

  • signed incidence matrix

  • concordance, discordance

  • agreement, disagreement

  • R

  • R package / library (review R discussions about this terminology)

  • data visualization

  • intersection, union, subtraction, buffer region

Citations to add

Luana Micallef, Pierre Dragicevic and Jean-Daniel Fekete (2012): Assessing the Effect of Visualizations on Bayesian Reasoning through Crowdsourcing. IEEE Transactions on Visualization and Computer Graphics, 18(12): 2536-2545. http://www.eulerdiagrams.org/eulerGlyphs, http://www.aviz.fr/bayes

  • eulerGlyphs - reference the original mammography study reference dataset.

  • Standard two-Venn publication approach

https://pmc.ncbi.nlm.nih.gov/articles/PMC12063414/ Figure 6C. Two Venn diagrams: "CMV-induced CRE target genes" "CMV-repressed CRE target genes" DEGs are not easily downloaded, they're in DOCX format tables. Skip.

prdf <- jamba::readOpenxlsx("~/Downloads/1-s2.0-S0896627318303684-mmc2.xlsx", sheet=1:6, startRow=3)
jamba::sdim(prdf)
lapply(prdf[1:6], head, 4)
prl <- lapply(jamba::nameVectorN(prdf), function(iname){
   idf <- prdf[[iname]];
   igenes <- unique(idf[[2]])
   jamba::nameVector(rep(1, length(igenes)), igenes)
})
prsetlist <- list("PAX6+"=c(prl[[1]], prl[[2]]),
"TBR2+"=c(prl[[3]], prl[[4]])
)

heatdfs <- jamba::readOpenxlsx("~/Downloads/13059_2025_3595_MOESM4_ESM.xlsx", startRow=2)
lapply(heatdfs, jamba::middle, 5)

cmvdfs <- jamba::readOpenxlsx("~/Downloads/13059_2025_3595_MOESM5_ESM.xlsx", startRow=2)
lapply(cmvdfs, jamba::middle, 5)

Todo 18jun2025

  • Add section "How to re-center the Venndir".

  • PARTIAL. Add favicon.ico. Confirm it works?

  • Describe Markdown formatting, link to CommonMark.

  • Add section describing overlap_type.

  • Show how to use patchwork to assemble panels.

  • Show how to add Google fonts to use in Venndir.

  • Consider example adding new JamPolygon to v@jps, to highlight one multi-overlap region with an outer border for example.

  • DONE. Define custom global figure size

  • DONE. Add R package citations

  • DONE. Add section for advanced grid manipulations

  • Show how to edit a grid attribute and plot the output.

  • Consider editing item label positions using grid object editing?