Visualization the output of ancombc2

[J5886]

Hi @FrederickHuangLin,

thanks for this wonderful differential tool, I've tried a lot to visualize the output of ancombc2 as a volcano plot but got an error

the command used is with(pp, plot("lfc_Statuscontrol", -log10("q_Statuscontrol"), pch=20, main="Volcano plot"))

Error in eval(substitute(expr), data, enclos = parent.frame()) : invalid 'envir' argument of type 'character

the output of ancombc2 (pp) Taxon lfc_Statuscontrol q_Statuscontrol g__Lachnospira 1.842487 0.0240705 g__Dorea 1.662488 0.0184713 g__Bifidobacterium -2.125457 0.0350155 g__Ruminococcus 2.184326 0.0225421 g__Clostridium -2.305637 0.0415318 g__Rothia -3.303175 0.0134374

I've followed the tutorial "ANCOM-BC Tutorial" part of Visualization for age df_age = res_prim %>% dplyr::select(taxon, ends_with("age")) df_fig_age = df_age %>% dplyr::filter(diff_age == 1) %>% dplyr::arrange(desc(lfc_age)) %>% dplyr::mutate(direct = ifelse(lfc_age > 0, "Positive LFC", "Negative LFC"), color = ifelse(passed_ss_age == 1, "aquamarine3", "black")) but, some data included in that command are not available in my output (the column passed_ss)

any suggestions are highly appreciated

Regards

[Maggie8888]

Could you please provide the information for your res_prim object ?