runs a Principal Component Analysis
runPCA(
gobject,
spat_unit = NULL,
feat_type = NULL,
expression_values = c("normalized", "scaled", "custom"),
reduction = c("cells", "feats"),
name = NULL,
feats_to_use = "hvf",
return_gobject = TRUE,
center = TRUE,
scale_unit = TRUE,
ncp = 100,
method = c("irlba", "exact", "random", "factominer"),
method_params = BiocParallel::SerialParam(),
rev = FALSE,
set_seed = TRUE,
seed_number = 1234,
verbose = TRUE,
...
)giotto object
spatial unit
feature type
expression values to use
cells or genes
arbitrary name for PCA run
subset of features to use for PCA
boolean: return giotto object (default = TRUE)
center data first (default = TRUE)
scale features before PCA (default = TRUE)
number of principal components to calculate (see details)
which implementation to use
BiocParallelParam object
do a reverse PCA
use of seed
seed number to use
verbosity of the function
additional parameters for PCA (see details)
giotto object with updated PCA dimension recuction
See runPCA and
PCA for more information about other parameters.
With the feats_to_use param, you can control which features are used to
calculate your PCA, which can be useful for making sure that your downstream
dimension reduction and clusterings are based on your features of interest.
feats_to_use = NULL: will use all features from the selected matrix
feats_to_use = <hvg name>: can be used to select a column name of
highly variable features, created by (see calculateHVF)
feats_to_use = c('geneA', 'geneB', ...): will use all manually provided features
By default the number of principle components that we calculate is 100, which may not encompass all the variation within the dataset. Setting ncp to NULL will calculate all the principle components.
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> cell_spatInfo_spatVector.shp
#> cell
#>
#> 3.2 read Giotto spatial centroid information
#> cell
#>
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#> skipped
#>
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#> "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
runPCA(g)
#> "hvf" column was found in the feats metadata information and will be
#> used to select highly variable features
#> Warning: ncp >= minimum dimension of x, will be set to
#> minimum dimension of x - 1
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
#> Warning: did not converge--results might be invalid!; try increasing work or maxit
#> > pca already exists and will be replaced with
#> new dimension reduction object
#> An object of class giotto
#> >Active spat_unit: cell
#> >Active feat_type: rna
#> [SUBCELLULAR INFO]
#> polygons : cell
#> [AGGREGATE INFO]
#> expression -----------------------
#> [cell][rna] raw normalized scaled
#> spatial locations ----------------
#> [cell] raw
#> spatial networks -----------------
#> [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#> [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#> [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#> [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images : alignment image
#>
#>
#> Use objHistory() to see steps and params used