diff --git a/README.Rmd b/README.Rmd index a716f93..57fab9b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,7 +13,7 @@ knitr::opts_chunk$set( ) ``` -# visiumStitched +# visiumStitched [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/issues) diff --git a/README.md b/README.md index d6e95d1..681da73 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# visiumStitched +# visiumStitched @@ -64,7 +64,7 @@ stopifnot(packageVersion("spatialLIBD") >= "1.17.8") ## Download the spot-level data, which is a SpatialExperiment object spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe") -#> 2024-07-24 14:40:50.071424 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 +#> 2024-07-26 14:06:21.739878 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 ## Explore the stitched data spe diff --git a/dev/.gitignore b/dev/.gitignore new file mode 100644 index 0000000..5fa9740 --- /dev/null +++ b/dev/.gitignore @@ -0,0 +1 @@ +logo.pdf diff --git a/dev/05_make_logo.R b/dev/05_make_logo.R new file mode 100644 index 0000000..1521740 --- /dev/null +++ b/dev/05_make_logo.R @@ -0,0 +1,20 @@ +library("spatialLIBD") + +## Grab SpatialExperiment with normalized counts +spe_norm <- fetch_data(type = "visiumStitched_brain_spe") + +## PRECAST k = 2 clusters +spe_norm$precast_k2 <- factor(spe_norm$precast_k2) +pdf(here::here("dev", "logo.pdf"), height = 7) +vis_clus( + spe_norm, + clustervar = "precast_k2", + is_stitched = TRUE, + colors = c( + "2" = "darkblue", + "1" = "gold", + "NA" = "red" + ), + spatial = FALSE +) +dev.off() diff --git a/man/figures/logo.png b/man/figures/logo.png new file mode 100644 index 0000000..16101fe Binary files /dev/null and b/man/figures/logo.png differ