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.
ProjectDim(
object,
reduction = "pca",
assay = NULL,
dims.print = 1:5,
nfeatures.print = 20,
overwrite = FALSE,
do.center = FALSE,
verbose = TRUE
)Arguments
- object
Seurat object
- reduction
Reduction to use
- assay
Assay to use
- dims.print
Number of dims to print features for
- nfeatures.print
Number of features with highest/lowest loadings to print for each dimension
- overwrite
Replace the existing data in feature.loadings
- do.center
Center the dataset prior to projection (should be set to TRUE)
- verbose
Print top genes associated with the projected dimensions
Value
Returns Seurat object with the projected values
Examples
data("pbmc_small")
pbmc_small
#> An object of class Seurat
#> 230 features across 80 samples within 1 assay
#> Active assay: RNA (230 features, 20 variable features)
#> 3 layers present: counts, data, scale.data
#> 2 dimensional reductions calculated: pca, tsne
pbmc_small <- ProjectDim(object = pbmc_small, reduction = "pca")
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 1
#> Positive: SDPR, PF4, PPBP, TUBB1, CA2, TREML1, MYL9, PGRMC1, RUFY1, PARVB
#> Negative: HLA-DPB1, HLA-DQA1, S100A9, S100A8, GNLY, RP11-290F20.3, CD1C, AKR1C3, IGLL5, VDAC3
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 2
#> Positive: HLA-DPB1, HLA-DQA1, S100A8, S100A9, CD1C, RP11-290F20.3, PARVB, IGLL5, MYL9, SDPR
#> Negative: GNLY, AKR1C3, VDAC3, PGRMC1, TUBB1, PF4, TREML1, RUFY1, CA2, PPBP
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 3
#> Positive: S100A9, S100A8, RP11-290F20.3, AKR1C3, PARVB, GNLY, PPBP, PGRMC1, MYL9, TUBB1
#> Negative: HLA-DQA1, CD1C, IGLL5, HLA-DPB1, RUFY1, PF4, VDAC3, SDPR, TREML1, CA2
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 4
#> Positive: IGLL5, RP11-290F20.3, VDAC3, PPBP, TUBB1, TREML1, PF4, CA2, PARVB, MYL9
#> Negative: CD1C, AKR1C3, S100A8, GNLY, HLA-DPB1, HLA-DQA1, S100A9, PGRMC1, RUFY1, SDPR
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
#> PC_ 5
#> Positive: MYL9, PARVB, IGLL5, TREML1, AKR1C3, PGRMC1, HLA-DPB1, S100A9, TUBB1, PF4
#> Negative: VDAC3, RP11-290F20.3, RUFY1, CD1C, HLA-DQA1, CA2, S100A8, PPBP, GNLY, SDPR
# Visualize top projected genes in heatmap
DimHeatmap(object = pbmc_small, reduction = "pca", dims = 1, balanced = TRUE)
#> Warning: Requested number is larger than the number of available items (20). Setting to 20.
