Cluster cells using a random walk approach.
doRandomWalkCluster(
gobject,
name = "random_walk_clus",
nn_network_to_use = "sNN",
network_name = "sNN.pca",
walk_steps = 4,
walk_clusters = 10,
walk_weights = NA,
return_gobject = TRUE,
set_seed = FALSE,
seed_number = 1234
)giotto object
name for cluster, default to "random_walk_clus"
type of NN network to use (kNN vs sNN), default to "sNN"
name of NN network to use, default to "sNN.pca"
number of walking steps, default = 4
number of final clusters, default = 10
cluster column defining the walk weights
boolean: return giotto object (default = TRUE)
set seed (default = FALSE)
number for seed
giotto object with new clusters appended to cell metadata
See cluster_walktrap function from the igraph
package in R for more information.
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
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
g <- doRandomWalkCluster(g)
pDataDT(g)
#> cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus
#> <char> <int> <int> <num> <num> <num>
#> 1: AACTCGATGGCGCAGT-1 1 265 41.79811 1057.9308 2
#> 2: GGCTGGCTAGCTTAAA-1 1 279 44.00631 1064.7493 5
#> 3: GACGCCTGTTGCAGGG-1 1 219 34.54259 964.9294 2
#> 4: GAGGGCATCGCGTATC-1 1 294 46.37224 1142.7664 2
#> 5: TCAACACATTGGGTAA-1 1 261 41.16719 1063.3517 2
#> ---
#> 620: GGTAGTGCTCGCACCA-1 1 179 28.23344 768.4749 5
#> 621: AAGCTCGTGCCAAGTC-1 1 195 30.75710 756.0675 5
#> 622: TATTCAATTCTAATCC-1 1 247 38.95899 921.8264 5
#> 623: TTCAAAGTCTCTAGCC-1 1 384 60.56782 916.5929 6
#> 624: TTGAATATGGACTTTC-1 1 380 59.93691 912.3051 6
#> custom_leiden random_walk_clus
#> <num> <fctr>
#> 1: 4 2
#> 2: 3 2
#> 3: 3 5
#> 4: 3 2
#> 5: 3 5
#> ---
#> 620: 4 2
#> 621: 4 2
#> 622: 4 2
#> 623: 7 2
#> 624: 4 2