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License: Other
nyankomicro is a in-house package that aims to make the plots more beautiful.
License: Other
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。
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。
══ 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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