Seurat (version 2.3.4)

ProjectDim: Project Dimensional reduction onto full dataset

Description

Takes a pre-computed dimensional reduction (typically calculated on a subset of genes) and projects this onto the entire dataset (all genes). Note that the cell loadings will remain unchanged, but now there are gene loadings for all genes.

Usage

ProjectDim(object, reduction.type = "pca", dims.print = 1:5,
  dims.store = 30, genes.print = 30, replace.dim = FALSE,
  do.center = FALSE, do.print = TRUE, assay.type = "RNA")

Arguments

object

Seurat object

reduction.type

Reduction to use

dims.print

Number of dims to print genes for

dims.store

Number of dims to store (default is 30)

genes.print

Number of genes with highest/lowest loadings to print for each PC

replace.dim

Replace the existing data (overwrite object@dr$[e-mail]), not done by default.

do.center

Center the dataset prior to projection (should be set to TRUE)

do.print

Print top genes associated with the projected dimensions

assay.type

Data type, RNA by default. Can be changed for multimodal datasets (i.e. project a PCA done on RNA, onto CITE-seq data)

Value

Returns Seurat object with the projected values in object@dr$[e-mail]

Examples

# NOT RUN {
pbmc_small
pbmc_small <- ProjectDim(pbmc_small, reduction.type = "pca")
# Vizualize top projected genes in heatmap
DimHeatmap(pbmc_small,pc.use = 1,use.full = TRUE,do.balanced = TRUE,reduction.type = "pca")

# }