Table 2.

Summary of main visualization functions in EasyAmplicon

Plot	Script	Description	References
Boxplot	alpha_boxplot.R	The plot shows data distribution in each group. Dots represent each sample, and labeled letters indicate statistical significance among groups	[10]
Rarefaction curve	alpha_rare_curve.R	Richness of rarefied samples or groups from 1% to 100%	[10]
Venn diagram	sp_vennDiagram.sh	Visualizes common and unique elements among 2−5 groups	[53, 54]
Ordination scatter plot	beta_pcoa.R beta_cpcoa.R	Shows the results of dimensionality reduction	[55]
Heatmap	sp_pheatmap.sh compare_heatmap.sh	Shows distance or similarity matrix and deferential abundance features	[50, 56]
Stack plot	tax_stackplot.R	Shows taxonomic and functional composition in each sample or group	[57]
Cricular plot	tax_circlize.R	Shows taxonomic composition	[58]
Circle packing chart	tax_maptree.R	Shows the relations and relative abundance of taxonomic hierarchy	[59]
Volcano plot	compare_volcano.R	The dots in the plot show abundance and fold changes between two groups	[50]
Manhattan plot	compare_manhattan.sh	Shows taxonomy, abundance, and pattern between two groups	[60]