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How do CCA calculations use the first 10 Phylum/Genus?

Open makerer5 opened this issue 7 months ago • 3 comments

Hi I am using CCA analysis to calculate the relationship between the environmental factors and the top 10 Phylum/Genus, but I found that the RDA analysis can select the top 10 Phylum/Genus, but CCA doesn't seem to be able to select the top 10 Phylum/Genus freely. This is my RDA analysis code:

use Genus

t1$cal_ordination(method = "RDA", taxa_level = "Phylum")

select 10 features and adjust the arrow length

t1$trans_ordination(show_taxa = 10, adjust_arrow_length = TRUE, max_perc_env = 1.5, max_perc_tax = 1.5, min_perc_env = 0.2, min_perc_tax = 0.2)

t1$res_rda_trans is the transformed result for plot

t1$plot_ordination(plot_color = "Group",color_values = venn_colors) This is my CCA code:

CCA, canonical correspondence analysis

t1$cal_ordination(method = "CCA", taxa_level = "Genus") t1$trans_ordination(adjust_arrow_length = TRUE,show_taxa = 10,max_perc_env = 1.5, max_perc_tax = 1.5, min_perc_env = 0.2, min_perc_tax = 0.2) t1$plot_ordination(plot_color = "Group", plot_shape = "Group", color_values = venn_colors) How does the CCA analysis select the top 10 Phylum/Genus?

makerer5 avatar Jul 18 '24 13:07 makerer5