smfishHmrf.generate.centroid.it: Generate cluster centroids, where input is a file.
In smfishHmrf: Hidden Markov Random Field for Spatial Transcriptomic Data

Description Usage Arguments Details Value Examples

This function generates cluster centroids from applying kmeans. It accepts an expression matrix file as input.

smfishHmrf.generate.centroid.it(
  expr_file,
  par_k,
  par_seed = -1,
  nstart,
  name = "test",
  output_dir = "."
)

`expr_file`	expression matrix file. The expression file should be a space-separated file. The rows are genes. The columns are cells. There is no header row. The first column is a gene index (ranges from 1 to the number of genes). Note the first column is not gene name.
`par_k`	number of clusters
`par_seed`	random generator seed (-1 if no fixing). Change the par_seed to vary the initialization.
`nstart`	number of starts (kmeans). It is recommended to set nstart to at least 100 (preferrably 1000).
`name`	name of this run
`output_dir`	output directory; where to store the kmeans results

Note that after running kmeans step, the function also automatically saves the kmeans results to the output_dir directory. The results will be found in two files:

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

where {} refers to the value of parameters.

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

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mem_file = system.file("extdata", "ftest.expression.txt", package="smfishHmrf")
kk = smfishHmrf.generate.centroid.it(mem_file, par_k=9, par_seed=100, 
    nstart=100, name="test", output_dir=tempdir())