From 257cfe50a53ebc0bba51ca58d493272a29e28bb5 Mon Sep 17 00:00:00 2001 From: Wubing Zhang Date: Tue, 12 Nov 2024 11:38:13 -0800 Subject: [PATCH] renew the googledrive site in the documentation --- docs/articles/Recovery_scRNA.html | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/articles/Recovery_scRNA.html b/docs/articles/Recovery_scRNA.html index 2587c47..4975cb0 100644 --- a/docs/articles/Recovery_scRNA.html +++ b/docs/articles/Recovery_scRNA.html @@ -88,7 +88,7 @@

OverviewsuppressPackageStartupMessages(library(Seurat)) suppressPackageStartupMessages(library(data.table)) suppressPackageStartupMessages(library(googledrive)) -library(SpatialEcoTyper) +library(SpatialEcoTyper)

Data preparation @@ -96,10 +96,10 @@

Data preparationThe recovery process requires a normalized gene expression matrix and a vector of cell type annotations.

Starting from a Seurat object -

A seurat object for the demo data can be accessed from WU2161_seurat_obj.rds.

+

A seurat object for the demo data can be accessed from WU2161_seurat_obj.rds.

 drive_deauth() # Disable Google sign-in requirement
-drive_download(as_id("17356t3n4vY581hogyi0Gmz4Sj5v804Vz"), "WU2161_seurat_obj.rds", overwrite = TRUE)
+drive_download(as_id("11ORWQxxWCNUtceEDwu2IyBpDMa6P-bxS"), "WU2161_seurat_obj.rds", overwrite = TRUE)

First, load the seurat object into R:

 # Load the seurat object
@@ -113,7 +113,7 @@ 
Data preparation
 # Cell type annotations
 unique(obj$CellType)
-
## [1] "Macrophage" "B"          "CD4T"       "CD8T"       "Neuron"    
+
## [1] "Macrophage" "B"          "CD4T"       "CD8T"       "Other"     
 ## [6] "Fibroblast" "Epithelial" "Plasma"

 
Next, normalize the gene expression data using SCTransform
 or NormalizeData.
@@ -159,7 +159,7 @@ 
Data preparation
 table(ctann)

 
## ctann
-##          B       CD4T       CD8T Epithelial Fibroblast Macrophage     Neuron 
+##          B       CD4T       CD8T Epithelial Fibroblast Macrophage      Other 
 ##         97        138        425        121         44        374         91 
 ##     Plasma 
 ##         47

@@ -220,10 +220,10 @@ 
Data preparationctann = ctann[match(colnames(normdata), rownames(ctann)), 1]
 table(ctann)
## ctann
-##          B       CD4T       CD8T Epithelial Fibroblast Macrophage     Plasma 
-##         97        138        425        121         44        374         47 
-##    Unknown 
-##         91
+## B CD4T CD8T Epithelial Fibroblast Macrophage Other +## 97 138 425 121 44 374 91 +## Plasma +## 47
@@ -325,7 +325,7 @@

Session info## [8] base ## ## other attached packages: -## [1] SpatialEcoTyper_1.0.0 NMF_0.28 Biobase_2.64.0 +## [1] SpatialEcoTyper_0.0.5 NMF_0.28 Biobase_2.64.0 ## [4] BiocGenerics_0.50.0 cluster_2.1.6 rngtools_1.5.2 ## [7] registry_0.5-1 RANN_2.6.2 Matrix_1.7-0 ## [10] googledrive_2.1.1 data.table_1.16.0 Seurat_5.1.0