Description Usage Arguments Value Examples
View source: R/cluster_analysis.R
Perform clustering analysis for a range of hyperparameter (KNN Ratios) values and assess clustering quality relative to simulation analysis of shuffled data.
1 2 3 4 | cluster.analysis(environment, knn.ratios = c(0.01, 0.05, 0.1),
nShuffleRuns = 10, shuffledKNN = 10, loadPreviousKnn = T,
rerun = F, deleteCache = F, mem = "4GB", time = "0:15:00",
plot = T, local = F)
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environment |
|
knn.ratios |
range of KNN parameters to scan (corresponding to different resolutions) |
nShuffleRuns |
number of shuffled clustering analyses to perform per KNN threshold |
shuffledKNN |
number of closest KNN shuffled analyses to include in background clustering quality computation |
loadPreviousKnn |
whether to load previous analysis results |
rerun |
whether to rerun the analysis rather than load from cache |
deleteCache |
whether to delete cache files |
mem |
HPC memory |
time |
HPC time |
plot |
whether to plot the clustering qualities compared to shuffled |
local |
whether to run jobs locally rather than using distributed slurm system |
environment
parameter containing clustering assignment and provisional cluster names
1 2 3 4 5 | LCMV1 <- setup_LCMV_example()
LCMV1 <- get.variable.genes(LCMV1, min.mean = 0.1, min.frac.cells = 0,
min.dispersion.scaled = 0.1)
LCMV1 <- PCA(LCMV1)
LCMV1 <- cluster.analysis(LCMV1)
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