smfishHmrf.generate.centroid.use.exist: Use existing cluster centroids
In smfishHmrf: Hidden Markov Random Field for Spatial Transcriptomic Data

Description Usage Arguments Value Examples

This function assumes that cluster centroids have already been generated from previously applying kmeans on the dataset. The results should have been saved. It will load cluster centroids from existing clustering result files. The results should be found in input_dir directory. The function looks for the following two kmeans result files:

{input_dir}/k_{par_k}/f{name}.gene.ALL.centroid.txt
{input_dir}/k_{par_k}/f{name}.gene.ALL.kmeans.txt

where {} refers to the value of parameters down below

1	smfishHmrf.generate.centroid.use.exist(name = "test", input_dir = ".", par_k)

`name`	name of this run
`input_dir`	input directory
`par_k`	number of clusters

A kmeans object which is a list with centers and cluster fields

1 2	kmeans_results = system.file("extdata", package="smfishHmrf") kk = smfishHmrf.generate.centroid.use.exist(name="test", input_dir=kmeans_results, par_k=9)