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silhouette function (RStudio)

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RStudio silhouette function
Silhouette Function, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/silhouette+function/silhouette+function/pm38782729-59-2-4
Average 90 stars, based on 1 article reviews

silhouette function - by Bioz Stars, 2026-10

90/100 stars

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Article Title: Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs.
Article Snippet: The function “silhouette” in RStudio was used to perform the Silhouette analysis and the functions “hclust” and “cutree” in RStudio wer e used to calculate the hier archical clustering of samples, both based on species-level bacterial composition and in particular Bray–Curtis dissimilarity matrix.

Article Title: Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs
Article Snippet: The function “silhouette” in RStudio was used to perform the Silhouette analysis and the functions “hclust” and “cutree” in RStudio were used to calculate the hierarchical clustering of samples, both based on species-level bacterial composition and in particular Bray–Curtis dissimilarity matrix.

Article Title: BNA Festival of Neuroscience 2019
Article Snippet: Clustering will be carried out on R Studio, with the silhouette function being used to determine the optimal number of clusters.

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a Surgery for recording l/vlPAG vgat calcium transients (top). Example l/vlPAG vgat traces (bottom). b Order of assays. c L/vlPAG vgat activity centered at eating onset (cricket assay n = 223 neurons; walnut assay n = 204 neurons). d Representation of behaviors in principal component space (PC) during cricket hunting (see example on left). Clustering quality was measured by silhouette score, which was higher than the chance level of zero (dotted red line) ( n = 4 mice; one-sample two-tailed t -test, t-statistic = 2.79, p = 0.059). e Same as d , but for walnut ( n = 4 mice; one-one-sample two-tailed t -test, t-statistic = 14.37, p = 0.001). f Behaviors were decoded above chance (red dotted line) ( n = 4 mice; one-sample two-tailed t -test, cricket t-statistics: approach = 3.87, p = 0.031; eat = 5.59, p = 0.011; walnut t-statistics: approach = 4.75, p = 0.018, eat = 7.53, p = 0.005). g Cells co-registered across assays. h Mahalanobis distance between points from two clusters that display higher overlap (left panel with light and dark blue points) and two clusters that are well-separated (right panel with light and dark green points). i Mahalanobis distance between approach and eating clusters across the cricket and walnut assays in n-dimensions ( n = # of co-registered neurons). The distance between eating clusters across assays is smaller than the distance between approach clusters, indicating the representation of eating is more conserved than food approach (approach sample n = 527 time points, eat sample n = 1958 time points; two-tailed Wilcoxon rank-sum test, z-score = 22.88, p < 0.001). j Same as d , but for co-registered cells, showing conserved representation of behaviors across assays ( n = 4 mice; one-one-sample two-tailed t -test, t-statistic = 4.22, p = 0.024). k The distance between individual points and cluster center is smaller in the eating cluster than the approach cluster, indicating the representation of eating is more conserved across assays (approach sample n = 1049 time points, eat sample n = 5492 time points; two-tailed Wilcoxon rank-sum two-tailed test, z-score = 10.35, p < 0.001). *** p < 0.001, ** p < 0.01, * p < 0.05, † p = 0.059. Data are presented as mean values +/- SEM. Source data are provided as a Source Data File.

Journal: Nature Communications

Article Title: Control of feeding by a bottom-up midbrain-subthalamic pathway

doi: 10.1038/s41467-024-46430-5

Figure Lengend Snippet: a Surgery for recording l/vlPAG vgat calcium transients (top). Example l/vlPAG vgat traces (bottom). b Order of assays. c L/vlPAG vgat activity centered at eating onset (cricket assay n = 223 neurons; walnut assay n = 204 neurons). d Representation of behaviors in principal component space (PC) during cricket hunting (see example on left). Clustering quality was measured by silhouette score, which was higher than the chance level of zero (dotted red line) ( n = 4 mice; one-sample two-tailed t -test, t-statistic = 2.79, p = 0.059). e Same as d , but for walnut ( n = 4 mice; one-one-sample two-tailed t -test, t-statistic = 14.37, p = 0.001). f Behaviors were decoded above chance (red dotted line) ( n = 4 mice; one-sample two-tailed t -test, cricket t-statistics: approach = 3.87, p = 0.031; eat = 5.59, p = 0.011; walnut t-statistics: approach = 4.75, p = 0.018, eat = 7.53, p = 0.005). g Cells co-registered across assays. h Mahalanobis distance between points from two clusters that display higher overlap (left panel with light and dark blue points) and two clusters that are well-separated (right panel with light and dark green points). i Mahalanobis distance between approach and eating clusters across the cricket and walnut assays in n-dimensions ( n = # of co-registered neurons). The distance between eating clusters across assays is smaller than the distance between approach clusters, indicating the representation of eating is more conserved than food approach (approach sample n = 527 time points, eat sample n = 1958 time points; two-tailed Wilcoxon rank-sum test, z-score = 22.88, p < 0.001). j Same as d , but for co-registered cells, showing conserved representation of behaviors across assays ( n = 4 mice; one-one-sample two-tailed t -test, t-statistic = 4.22, p = 0.024). k The distance between individual points and cluster center is smaller in the eating cluster than the approach cluster, indicating the representation of eating is more conserved across assays (approach sample n = 1049 time points, eat sample n = 5492 time points; two-tailed Wilcoxon rank-sum two-tailed test, z-score = 10.35, p < 0.001). *** p < 0.001, ** p < 0.01, * p < 0.05, † p = 0.059. Data are presented as mean values +/- SEM. Source data are provided as a Source Data File.

Article Snippet: The silhouette score was calculated across these three behavioral clusters using the Matlab function ‘silhouette’.

Techniques: Activity Assay, Two Tailed Test