plotValidate {GenomicSuperSignature} | R Documentation |
There are three main information on the graph:
x-axis : Pearson correlation coefficient. Higher value means that test dataset and RAV is more tightly associated with.
y-axis : Silhouette width representing the quality of RAVs.
size : The number of studies in each RAV. (= cluster size)
color : Test dataset's PC number that validate each RAV. Because we used top 8 PCs of the test dataset, there are 8 categories.
plotValidate( val_all, minClusterSize = 2, swFilter = FALSE, minSilhouetteWidth = 0, interactive = FALSE, minClSize = NULL, maxClSize = NULL, colorPalette = "Dark2" )
val_all |
Output from validate function. |
minClusterSize |
The minimum size of clusters to be included in the plotting. Default value is 2, so any single-element clusters are excluded. |
swFilter |
If |
minSilhouetteWidth |
A minimum average silhouette width to be plotted.
Only effective under |
interactive |
If set to |
minClSize |
The minimum number of PCs in the clusters you want. |
maxClSize |
The maximum number of PCs in the clusters you want. |
colorPalette |
Default is |
a ggplot object
data(miniRAVmodel) library(bcellViper) data(bcellViper) val_all <- validate(dset, miniRAVmodel) plotValidate(val_all)