add singlecell and xen integration

drieslab · Nov 25, 2024 · c75057a · c75057a
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diff --git a/vignettes/images/janesick_sc/10_scran.png b/vignettes/images/janesick_sc/10_scran.png
diff --git a/vignettes/images/janesick_sc/11_gini.png b/vignettes/images/janesick_sc/11_gini.png
diff --git a/vignettes/images/janesick_sc/12_celltypes.png b/vignettes/images/janesick_sc/12_celltypes.png
diff --git a/vignettes/images/janesick_sc/1_mito.png b/vignettes/images/janesick_sc/1_mito.png
diff --git a/vignettes/images/janesick_sc/2_mito.png b/vignettes/images/janesick_sc/2_mito.png
diff --git a/vignettes/images/janesick_sc/3_doublet.png b/vignettes/images/janesick_sc/3_doublet.png
diff --git a/vignettes/images/janesick_sc/4_filter_combinations.png b/vignettes/images/janesick_sc/4_filter_combinations.png
diff --git a/vignettes/images/janesick_sc/5_scree.png b/vignettes/images/janesick_sc/5_scree.png
diff --git a/vignettes/images/janesick_sc/6_umap.png b/vignettes/images/janesick_sc/6_umap.png
diff --git a/vignettes/images/janesick_sc/7_overclust.png b/vignettes/images/janesick_sc/7_overclust.png
diff --git a/vignettes/images/janesick_sc/8_mclus.png b/vignettes/images/janesick_sc/8_mclus.png
diff --git a/vignettes/images/janesick_sc/9_dimfeats.png b/vignettes/images/janesick_sc/9_dimfeats.png
diff --git a/vignettes/images/xenium_breast_cancer/dimfeats.png b/vignettes/images/xenium_breast_cancer/dimfeats.png
diff --git a/vignettes/images/xenium_breast_cancer/join_celltypes.png b/vignettes/images/xenium_breast_cancer/join_celltypes.png
diff --git a/vignettes/images/xenium_breast_cancer/join_pca.png b/vignettes/images/xenium_breast_cancer/join_pca.png
diff --git a/vignettes/images/xenium_breast_cancer/join_scree.png b/vignettes/images/xenium_breast_cancer/join_scree.png
diff --git a/vignettes/images/xenium_breast_cancer/join_transfer.png b/vignettes/images/xenium_breast_cancer/join_transfer.png
diff --git a/vignettes/images/xenium_breast_cancer/join_umap.png b/vignettes/images/xenium_breast_cancer/join_umap.png
diff --git a/vignettes/images/xenium_breast_cancer/xen_transfer.png b/vignettes/images/xenium_breast_cancer/xen_transfer.png
diff --git a/vignettes/janesick_scrna.Rmd b/vignettes/janesick_scrna.Rmd
diff --git a/vignettes/xenium_breast_cancer.rmd b/vignettes/xenium_breast_cancer.rmd
diff --git a/vignettes/xenium_lung_cancer.Rmd b/vignettes/xenium_lung_cancer.Rmd
@@ -0,0 +1,50 @@
+---
+title: "Xenium FFPE Human Lung Cancer with Multimodal Cell Segmentation"
+output: 
+  html_document:
+    number_sections: true
+    toc: true
+pkgdown:
+  as_is: true
+vignette: >
+  %\VignetteIndexEntry{Xenium FFPE Human Lung Cancer with Multimodal Cell Segmentation}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+# Install extra package: _arrow_
+
+Xenium datasets requires arrow with 'ZTSD' support to be installed to work with parquet files.
+This is optional if you want to use a different format for the tabular data.
+```{r, eval = FALSE}
+if (!requireNamespace("arrow", quietly = TRUE)) {
+  # install with compression library needed for 10x parquet files
+  Sys.setenv(ARROW_WITH_ZSTD = "ON") 
+  install.packages("arrow", repos = c("https://apache.r-universe.dev"))
+}
+
+# check arrow_info() to see that zstd support should be TRUE
+# See https://arrow.apache.org/docs/r/articles/install.html for details
+zstd <- arrow::arrow_info()$capabilities[["zstd"]]
+if (!zstd) {
+  stop("arrow needs to be reinstalled with the command above.")
+}
+```
+
+
+
+
+```{r, eval=FALSE}
+library(Giotto)
+
+# 1. ** SET WORKING DIRECTORY WHERE PROJECT OUPUTS WILL SAVE TO **
+results_folder = '/path/to/save/directory/'
+
+# 2. Create Giotto instructions
+# Directly saving plots to the working directory without rendering them in the editor saves time.
+instrs = createGiottoInstructions(save_dir = results_folder,
+                                  save_plot = TRUE,
+                                  show_plot = FALSE,
+                                  return_plot = FALSE)
+```