Multi parameter aggregator version of
silhouetteRank
silhouetteRankTest(
gobject,
expression_values = c("normalized", "scaled", "custom"),
subset_genes = NULL,
overwrite_input_bin = TRUE,
rbp_ps = c(0.95, 0.99),
examine_tops = c(0.005, 0.01, 0.05, 0.1, 0.3),
matrix_type = "dissim",
num_core = 4,
parallel_path = "/usr/bin",
output = NULL,
query_sizes = 10L,
verbose = FALSE
)
giotto object
expression values to use
only run on this subset of genes
overwrite input bin
fractional binarization thresholds
top fractions to evaluate with silhouette
type of matrix
number of cores to use
path to GNU parallel function
output directory
size of query
be verbose
data.table with spatial scores
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
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#>
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
silhouetteRankTest(g)
#> Error: package 'EnvStats' is not yet installed
#>
#> To install:
#> install.packages(c("EnvStats"))