silhouetteRankTest

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
)

Arguments

gobject

giotto object

expression_values

expression values to use

subset_genes

only run on this subset of genes

overwrite_input_bin

overwrite input bin

rbp_ps

fractional binarization thresholds

examine_tops

top fractions to evaluate with silhouette

matrix_type

type of matrix

num_core

number of cores to use

parallel_path

path to GNU parallel function

output

output directory

query_sizes

size of query

verbose

be verbose

Value

data.table with spatial scores

Examples

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"))