卡在ggpicrust2pathway_annotation

Question

我正在 R 中运行 ggpicrust2 来绘制 picrust 结果，但我没有得到绘图，因为 pathway_annotation 函数无法处理我的数据。当我练习示例时，我没有遇到问题，但是当注释我的数据时，输出没有任何注释（参见屏幕截图）。任何有关发生这种情况的可能原因的建议都将受到欢迎。我正在运行这段代码：

abundance_file <- "path/to/KO enrichment - filtered.tsv"

metadata <- read_delim("path/to/metadata.txt",
                       delim = "\t",
                       escape_double = FALSE,
                       trim_ws = TRUE
)


abundance_data <- read_delim(abundance_file, delim = "\t", col_names = TRUE, trim_ws = TRUE)

kegg_abundance <- ko2kegg_abundance(data = abundance_data)

daa_results_df <- pathway_daa(abundance = kegg_abundance, metadata = metadata, group = "Site", daa_method = "DESeq2", select = NULL, p.adjust = "BH", reference = NULL)

daa_annotated_results_df <- pathway_annotation(pathway = "KO", daa_results_df = daa_results_df, ko_to_kegg = TRUE)

Answer 1

当我尝试通过从pathway_annotation文档中的示例制作数据集来复制您的问题时：

library(ggpicrust2)
data(daa_results_df)
pathway_annotation(file = NULL,
                              pathway = "KO",
                              daa_results_df = daa_results_df,
                              ko_to_kegg = TRUE)

and tweaking data_results_df to look like your screenshot

data(daa_results_df)
daa_results_df$method <- "DESeq2"
daa_results_df$group1 <- "SG"
daa_results_df$group3 <- "VC"
daa_results_df$p_values <- runif(194, 0, 1)^5
daa_results_df$p_adjust <- runif(194, 0, 1)^6
daa_results_df$pathway_name <- NA
daa_results_df$pathway_description <- NA
daa_results_df$pathway_class <- NA
daa_results_df$pathway_map <- NA

我注意到我可以通过使一些 data_results_df$p_adjust 非常小来打破它：daa_results_df$p_adjust <- runif(194, 0, 1)^6 makes it fail, but daa_results_df$p_adjust <- runif(194, 0, 1)^3 works.