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### R code from vignette source 'VAM_pbmc_small_sctransform.Rnw'
###################################################
### code chunk number 1: VAM_pbmc_small_sctransform.Rnw:15-16
###################################################
library(VAM)
###################################################
### code chunk number 2: VAM_pbmc_small_sctransform.Rnw:23-30
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
SeuratObject::pbmc_small
gene.names = rownames(SeuratObject::pbmc_small)
gene.names[1:5]
} else {
message("Seurat package not available! Not executing associated vignette content.")
}
###################################################
### code chunk number 3: VAM_pbmc_small_sctransform.Rnw:35-44
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
pbmc_sctransform = Seurat::SCTransform(SeuratObject::pbmc_small, verbose=F)
# Compute PCA and UMAP on the normalized values
pbmc_sctransform = Seurat::RunPCA(pbmc_sctransform, npcs=10)
pbmc_sctransform = Seurat::RunUMAP(pbmc_sctransform, dims = 1:10)
Seurat::VariableFeatures(pbmc_sctransform)[1:5]
} else {
message("Seurat package not available! Not executing associated vignette content.")
}
###################################################
### code chunk number 4: VAM_pbmc_small_sctransform.Rnw:51-67
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
gene.set.name = "Test"
gene.ids = c("NKG7", "PPBP", "GNLY", "PF4", "GNG11")
# Create a collection list for this gene set
gene.set.id.list = list()
gene.set.id.list[[1]] = gene.ids
names(gene.set.id.list)[1] = gene.set.name
gene.set.id.list
# Create the list of gene indices required by vamForSeurat()
(gene.set.collection = createGeneSetCollection(gene.ids=gene.names,
gene.set.collection=gene.set.id.list))
gene.indices = gene.set.collection[[1]]
(gene.names = gene.names[gene.indices])
} else {
message("Seurat package not available! Not executing associated vignette content.")
}
###################################################
### code chunk number 5: VAM_pbmc_small_sctransform.Rnw:74-81
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
pbmc.vam = vamForSeurat(seurat.data=pbmc_sctransform,
gene.set.collection=gene.set.collection,
center=F, gamma=T, sample.cov=F, return.dist=T)
} else {
message("Seurat package not available! Not executing associated vignette content.")
}
###################################################
### code chunk number 6: VAM_pbmc_small_sctransform.Rnw:86-92
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
pbmc.vam@assays$VAMdist@data[1,1:10]
pbmc.vam@assays$VAMcdf@data[1,1:10]
} else {
message("Seurat package not available! Not executing associated vignette content.")
}
###################################################
### code chunk number 7: VAM_pbmc_small_sctransform.Rnw:99-110
###################################################
if (requireNamespace("Seurat", quietly=TRUE)) {
Seurat::DefaultAssay(object = pbmc.vam) = "VAMcdf"
Seurat::FeaturePlot(pbmc.vam, reduction="tsne", features=gene.set.name)
} else {
message("Seurat package not available! Not executing associated vignette content.")
par(mar = c(0,0,0,0))
plot(c(0, 1), c(0, 1), ann = F, bty = 'n', type = 'n', xaxt = 'n', yaxt = 'n')
text(x = 0.5, y = 0.5,paste("Seurat package not available!\n",
"FeaturePlot not generated."),
cex = 1.6, col = "black")
}
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