Complex UpSet plots
2020-11-15
Last updated: 2020-11-15
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Knit directory: muse/
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Following this tutorial. Firstly, install the package.
devtools::install_github("krassowski/complex-upset")
install.packages("ggplot2movies")The example uses the movies dataset from ggplot2movies, so make sure you have that package installed too.
movies <- as.data.frame(ggplot2movies::movies)
dim(movies)[1] 58788 24The example will plot the overlap of genres of movies.
genres <- colnames(movies)[18:24]
head(genres)[1] "Action" "Animation" "Comedy" "Drama" "Documentary"
[6] "Romance" Keep only movies with MPAA ratings.
movies %>% filter(mpaa != "") -> moviesNow to create the UpSet plot.
upset(movies,
genres,
name = 'genre',
width_ratio = 0.1,
min_size = 10)[1] "Converting non-logical columns to binary: Action, Animation, Comedy, Drama, Documentary, Romance, Short"
[1] "Dropping empty groups: Short"
Base annotation.
upset(
movies,
genres,
base_annotations = list(
'Intersection size' = intersection_size(
counts = FALSE,
aes = aes(fill = mpaa)
)
),
width_ratio = 0.1,
min_size = 10
)[1] "Converting non-logical columns to binary: Action, Animation, Comedy, Drama, Documentary, Romance, Short"
[1] "Dropping empty groups: Short"
Add the distribution of ratings.
upset(
movies,
genres,
annotations = list(
'Rating'=list(
aes=aes(x=intersection, y=rating),
geom=list(
# checkout ggbeeswarm::geom_quasirandom for better results!
geom_jitter(aes(color=log10(votes))),
geom_violin(width=1.1, alpha=0.5)
)
)
),
min_size=10,
width_ratio=0.1
) +
ggtitle("Movies")[1] "Converting non-logical columns to binary: Action, Animation, Comedy, Drama, Documentary, Romance, Short"
[1] "Dropping empty groups: Short"Warning: position_dodge requires non-overlapping x intervals
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ComplexUpset_0.5.20 ggplot2movies_0.0.1 forcats_0.5.0
[4] stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4
[7] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4
[10] ggplot2_3.3.2 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.19 haven_2.3.1 colorspace_2.0-0
[5] vctrs_0.3.4 generics_0.1.0 htmltools_0.5.0 yaml_2.2.1
[9] rlang_0.4.8 later_1.1.0.1 pillar_1.4.6 withr_2.3.0
[13] glue_1.4.2 DBI_1.1.0 dbplyr_2.0.0 modelr_0.1.8
[17] readxl_1.3.1 lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0
[21] cellranger_1.1.0 rvest_0.3.6 evaluate_0.14 labeling_0.4.2
[25] knitr_1.30 httpuv_1.5.4 fansi_0.4.1 broom_0.7.2
[29] Rcpp_1.0.5 promises_1.1.1 backports_1.2.0 scales_1.1.1
[33] jsonlite_1.7.1 farver_2.0.3 fs_1.5.0 hms_0.5.3
[37] digest_0.6.27 stringi_1.5.3 rprojroot_1.3-2 grid_4.0.2
[41] cli_2.1.0 tools_4.0.2 magrittr_1.5 patchwork_1.1.0
[45] crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.1
[49] xml2_1.3.2 reprex_0.3.0 lubridate_1.7.9 assertthat_0.2.1
[53] rmarkdown_2.5 httr_1.4.2 rstudioapi_0.13 R6_2.5.0
[57] git2r_0.27.1 compiler_4.0.2