Add some examples in the wild and reference to Lex et al in the descr…

…iption field

DESCRIPTION

@@ -8,6 +8,7 @@ Authors@R: person(
 Description: UpSet plots are an improvement over Venn Diagram for set overlap visualizations.
     Striving to bring the best of the 'UpSetR' and 'ggplot2', this package offers a way to create
     complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'.
+    For introduction to UpSet concept, see Lex et al. (2014) <doi:10.1109/TVCG.2014.2346248>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 URL: https://github.com/krassowski/complex-upset, https://krassowski.github.io/complex-upset/

README.md

@@ -87,6 +87,19 @@ Use whichever tool you find the most useful for your particular use. The rationa
 
 For the interactive use, check out the [VCG/upset](https://github.com/VCG/upset). Regardless of the tool chosen, you may want to cite [(Lex et al, 2014)](https://dx.doi.org/10.1109/TVCG.2014.2346248) when using UpSet plots, especially in fields still dominated by Venn diagrams.
 
+## Get inspired
+
+Here are example publications and preprints including figures generated with this library:
+
+- Martín-Martín et al. (2020). [Google Scholar, Microsoft Academic, Scopus, Dimensions, Web of Science, and OpenCitations’ COCI: a multidisciplinary comparison of coverage via citations](https://doi.org/10.1007/s11192-020-03690-4), *Scientometrics*: [Figure 2](https://link.springer.com/article/10.1007/s11192-020-03690-4#Fig2)
+- Green et al. (2020). [Metabolic correlates of late midlife cognitive function: findings from the 1946 British Birth Cohort](https://doi.org/10.1101/2020.11.23.20236463), *medRxiv*: [Figure 2](https://www.medrxiv.org/content/10.1101/2020.11.23.20236463v2.full#F2)
+- McDaniel et al. (2020). [Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics
+](https://doi.org/10.1101/2020.11.23.394700), *bioRxiv* [Figure 3](https://www.biorxiv.org/content/10.1101/2020.11.23.394700v1.full#F3)
+- Kozlowski et al. (2020). [Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita](https://doi.org/10.1101/2020.04.30.069948), *bioRxiv*: [Figure 7](https://www.biorxiv.org/content/10.1101/2020.04.30.069948v4.full#F7)
+- Swamy et al. (2020). [A long read optimized de novo transcriptome pipeline reveals novel ocular developmentally regulated gene isoforms and disease targets](https://doi.org/10.1101/2020.08.21.261644), *bioRxiv*: [Figure 4](https://www.biorxiv.org/content/10.1101/2020.08.21.261644v2.full#F4)
+
+The list is not meant to be exhaustive, but representative of applications to different fields, and of different usage ideas. You are welcome to add your own publication by [suggesting an edit](https://github.com/krassowski/complex-upset/edit/master/README.md).
+
 ## Testing
 
 The unit tests are run with testhat, and the visual "doppelganger" tests use vdiffr.

scripts/document.sh

@@ -6,7 +6,7 @@ cd vignettes
 cd ..
 for v in Examples_Python Examples_R
 do
-    rm -r "vignettes/${v}_files"
+    rm -rf "vignettes/${v}_files"
     jupyter nbconvert  --to markdown "vignettes/${v}.ipynb" 
     mv "vignettes/${v}.md" "vignettes/${v}.Rmd"
     sed 's/```r/```{r eval=FALSE}/g' "vignettes/${v}.Rmd" -i
@@ -16,9 +16,9 @@ do
     sed -i "1s/^/---\ntitle: \"${title}\"\nvignette: >\n  %\\\\VignetteEngine{knitr::rmarkdown}\n  %\\\\VignetteIndexEntry{${title}}\n  %\\\\usepackage[utf8]{inputenc}\n---\n/" "vignettes/${v}.Rmd"
 done
 rm -rf docs/articles
-Rscript -e 'pkgdown::build_site()'
 echo "Compressing images"
 for v in Examples_Python Examples_R
 do
-    trimage -q -d "vignettes/${v}_files"
+    trimage -q -d "vignettes/${v}_files" || true
 done
+Rscript -e 'pkgdown::build_site()'