Fig 1.
A: Simulation setting 1. The first line shows the true pattern and two-dimensional representations of samples from PCA, AC-PCA, PCoA(sp), AC-PCoA(sp) and aPCoA for one representative run. Samples are colored according to 3 types. The second line shows box plots of MANOVA F-statistic and NMI of k-means clustering on two-dimensional representations for 100 runs. B: Simulation setting 2. The first line shows the true pattern and two-dimensional sample representations from PCA, AC-PCA, PCoA(man), AC-PCoA(man) and aPCoA for one representative run. Samples are colored according to 10 types. The second line shows box plots of MANOVA F-statistic and NMI of k-means clustering for 100 runs. C: Simulation setting 3. The first line shows two-dimensional sample representations from PCA, AC-PCA, PCoA(bc), AC-PCoA(bc) and aPCoA for one representative run. Samples are colored according to 2 clinical groups. The second line shows box plots of MANOVA F-statistic and NMI of k-means clustering for 100 runs.
Fig 2.
Results of white oak tree data.
A: Two-dimensional representations of samples colored by continental origins after conducting AC-PCoA, PCoA, and aPCoA using six distance measures. B: MANOVA F-statistic, NMI of k-means clustering, and classification accuracy. Continental origins are set to be the true labels. MANOVA test, k-means clustering, and classification were conducted on two and three principal coordinates from PCoA, AC-PCoA, and aPCoA.
Fig 3.
Results of MBQC data (Dataset ‘A’).
A: Two-dimensional representations colored by specimens after conducting PCoA, AC-PCoA and aPCoA using Euclidean distance and Bray-Curtis distance. B: MANOVA F-statistic, NMI of k-means clustering, and classification accuracy. Specimens are set to be the true labels. MANOVA, k-means clustering, and classification were conducted on two and three principal coordinates from PCoA, AC-PCoA, and aPCoA.
Fig 4.
A: Two-dimensional plots colored by reference sample IDs after conducting PCoA, AC-PCoA and aPCoA, using four distance measures. B: MANOVA F-statistic, NMI of k-means clustering, and classification accuracy. Reference samples IDs are set to be the true label. MANOVA test, k-means clustering, and classification were conducted on two and three principal coordinates from PCoA, AC-PCoA, and aPCoA.
Fig 5.
A: Two-dimensional representations of samples colored by cell types after conducting PCoA, AC-PCoA and aPCoA using four distance measures. B: MANOVA F-statistic, NMI of k-means clustering, and classification accuracy. Cell types are set to be the true labels. MANOVA, k-means clustering, and classification were conducted on two and three principal coordinates from PCoA, AC-PCoA, and aPCoA.
Fig 6.
Results of human brain exon array data (window 5).
A: Two-dimensional plot colored by brain regions after conducting PCA, AC-PCA, PCoA, AC-PCoA and aPCoA, using four distance measures. B: MANOVA F-statistic, NMI of k-means clustering, and classification accuracy. Brain regions are set to be the true labels. MANOVA, k-means clustering, and classification were conducted on two and three principal coordinates from PCoA, AC-PCoA, and aPCoA.