View source: R/tuneCluster.block.spls.R

tuneCluster.block.spls | R Documentation |

This function identify the number of feautures to keep per component and thus by cluster in `mixOmics::block.spls`

by optimizing the silhouette coefficient, which assesses the quality of clustering.

```
tuneCluster.block.spls(
X,
Y = NULL,
indY = NULL,
ncomp = 2,
test.list.keepX = NULL,
test.keepY = NULL,
...
)
```

`X` |
list of numeric matrix (or data.frame) with features in columns and samples in rows (with samples order matching in all data sets). |

`Y` |
(optional) numeric matrix (or data.frame) with features in columns and samples in rows (same rows as |

`indY` |
integer, to supply if Y is missing, indicates the position of the matrix response in the list |

`ncomp` |
integer, number of component to include in the model |

`test.list.keepX` |
list of integers with the same size as X. Each entry corresponds to the different keepX value to test for each block of |

`test.keepY` |
only if Y is provideid. Vector of integer containing the different value of keepY to test for block |

`...` |
other parameters to be included in the spls model (see |

For each component and for each keepX/keepY value, a spls is done from these parameters. Then the clustering is performed and the silhouette coefficient is calculated for this clustering.

We then calculate "slopes" where keepX/keepY are the coordinates and the silhouette is the intensity. A z-score is assigned to each slope. We then identify the most significant slope which indicates a drop in the silhouette coefficient and thus a deterioration of the clustering.

`silhouette` |
silhouette coef. computed for every combinasion of keepX/keepY |

`ncomp` |
number of component included in the model |

`test.keepX` |
list of tested keepX |

`test.keepY` |
list of tested keepY |

`block` |
names of blocks |

`slopes` |
"slopes" computed from the silhouette coef. for each keepX and keepY, used to determine the best keepX and keepY |

`choice.keepX` |
best |

`choice.keepY` |
best |

`block.spls`

, `getCluster`

, `plotLong`

```
demo <- suppressWarnings(get_demo_cluster())
X <- list(X = demo$X, Z = demo$Z)
Y <- demo$Y
test.list.keepX <- list("X" = c(5,10,15,20), "Z" = c(2,4,6,8))
test.keepY <- c(2:5)
# tuning
tune.block.spls <- tuneCluster.block.spls(X= X, Y= Y,
test.list.keepX= test.list.keepX,
test.keepY= test.keepY,
mode= "canonical")
keepX <- tune.block.spls$choice.keepX
keepY <- tune.block.spls$choice.keepY
# final model
block.spls.res <- mixOmics::block.spls(X= X, Y= Y, keepX = keepX,
keepY = keepY, ncomp = 2, mode = "canonical")
# get clusters and plot longitudinal profile by cluster
block.spls.cluster <- getCluster(block.spls.res)
```

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