APAV: An advanced pangenome analysis and visualization toolkit
Fig 2
Visualization of pangenome analysis results in rice genomes.
(A) Proportion and distribution of core, softcore, distributed, and private genes. The proportion is shown in the pie chart and the distribution of gene numbers is shown in the bar plot. (B) Distribution of gene counts across accession groups. Each point in the figure represents a sample. (C) Pangenome size estimation. The pangenome and core-genome sizes are drawn for different accession groups of rice samples. (D) The heatmap of the PAV profile. The annotations above and to the left indicate the total number of genes. Each row of the heatmap is for a sample and each column is for a gene. (E) PCA results of the distributed gene PAV. Each point in the figure represents a sample. (F) Manhattan plot of phenotype association analyses for plant height. The five points with the highest p-values are marked with red dots. (G) An example illustrating the correlation between phenotypic groups and the gene PAV. (H) An example displaying phenotypic differences between presence and absence group samples.