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エラー: Can't subset columns that don't exist. x Column `threshold` doesn't exist.

microbiome_barplot(physeq, "Genus", c("sampling_date","colony"),plot_percent = 10)

とした際に発生。

原因は

taxotu_table <- otu_table(agg_phylo_rel) %>% as.data.frame() %>% rownames_to_column("ASV") %>%
        left_join(level_tax, by = ("ASV" = "ASV")) %>% select(-ASV) %>% group_by(across(all_of(level))) %>%
        summarise_all(sum) %>% remove_rownames() %>% column_to_rownames(level)
    taxotu_table$mean <- apply(taxotu_table, 1, mean)

にある。

原因としては、read countが0のサンプルが含まれる場合にmean colomnの値がNaNになるため、下流の計算がうまくいかずにthreshold colomnが生成されないこと。

解決案としては

physeq <- prune_samples(sample_sums(physeq)>=1000, physeq)

などを利用して、予めread countが0のサンプルを除去しておくこと。

のちに、read countによるfilteringをあらかじめerrorとして出力するように改訂すること。

questions

こんにちは、大阪大学生命機能研究科の須山と申します。現在16Sアンプリコン解析で こちらのnyankomicroのコードを使用しているのですが、データソースが異なるためだと思うのですが、うまく機能しない箇所があり、お伺い致したく思います。この場所で良いでしょうか。よろしくお願いいたします。

Error: `.data` must be a data frame without row names

══ Failed tests ════════════════════════════════════════════════════════════════
─ Error (test_microbiome_barplot.R:7:1): (code run outside of `test_that()`) ─
Error: `.data` must be a data frame without row names.
Backtrace:
    █
 1. ├─nyankomicro::microbiome_barplot(...) test_microbiome_barplot.R:7:0
 2. │ └─`%>%`(...)
 3. └─tibble::column_to_rownames(., level)

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