Perform Clustering on Time-Series Data

clusterTS performs clustering on time-series data and generates plots for visualization.

Usage

clusterTS(x, k = 5, pCut = NULL, twoCondition = FALSE)

Arguments

x

A numeric matrix with rows as features and columns as time points.

k

A numeric value specifying the number of clusters. Default is 5.

pCut

A numeric value specifying the probability cutoff for cluster membership. Default is NULL.

twoCondition

A logical value indicating if the data contains two conditions. Default is FALSE.

Value

A list containing:

cluster

A tibble with clustering information for each feature.

plot

A ggplot2 object for visualizing the clustering results.

Details

The function performs the following steps:

1. Sets a seed for reproducibility.

2. Removes rows with missing values.

3. Performs clustering using fuzzy C-means.

4. Filters clusters based on the probability cutoff if provided.

5. Generates plots for visualizing clustering results.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dia_example")
# Get SummarizedExperiment object
se <- dia_example[["Phosphoproteome"]]
colData(se) <- colData(dia_example)
seProcess <- preprocessPhos(seData = se, normalize = TRUE, impute = "QRILC")
#> Imputing along margin 2 (samples/columns).
result <- addZeroTime(seProcess, condition = "treatment", treat = "EGF",
zeroTreat = "1stCrtl", timeRange = c("20min","40min", "6h"))
# Get the numeric matrix
exprMat <- assay(result)
# Call the function
clusterTS(x = exprMat, k = 3)
#> $cluster
#> # A tibble: 345 × 7
#>    feature time                  value cluster   prob  cNum clusterNum   
#>    <fct>   <fct>                 <dbl> <chr>    <dbl> <int> <chr>        
#>  1 s198    Phospho_EGF_0min_rep2  13.3 cluster1 0.472    46 cluster1 (46)
#>  2 s198    Phospho_EGF_0min_rep3  13.1 cluster1 0.472    46 cluster1 (46)
#>  3 s198    Phospho_EGF_0min_rep1  13.1 cluster1 0.472    46 cluster1 (46)
#>  4 s337    Phospho_EGF_0min_rep2  12.5 cluster1 0.475    46 cluster1 (46)
#>  5 s337    Phospho_EGF_0min_rep3  12.6 cluster1 0.475    46 cluster1 (46)
#>  6 s337    Phospho_EGF_0min_rep1  14.3 cluster1 0.475    46 cluster1 (46)
#>  7 s9      Phospho_EGF_0min_rep2  10.7 cluster1 0.539    46 cluster1 (46)
#>  8 s9      Phospho_EGF_0min_rep3  10.7 cluster1 0.539    46 cluster1 (46)
#>  9 s9      Phospho_EGF_0min_rep1  10.4 cluster1 0.539    46 cluster1 (46)
#> 10 s204    Phospho_EGF_0min_rep2  12.0 cluster1 0.539    46 cluster1 (46)
#> # ℹ 335 more rows
#> 
#> $plot

#>