Difficulties with the ggpicrust2 package
0
0
Entering edit mode
10 days ago

Recently, I was reading about the ggpicrust2 package, a tool for interpreting functional prediction results. However, I was unable to run the script with my data. When executing the ggpicrust2 script (usage), the program returns an error message between the combination of metadata and the abundance file. However, I already checked and the names are the same.

If anyone who already uses the package can provide an example of the metadata they use to run the ggpicrust2 package and can help me, I would be extremely grateful.

Result of the error pointed out by the program during the execution of the script.

#Load Packages
library(readr)
library(ggpicrust2)
library(tibble)
library(tidyverse)
library(ggprism)
library(patchwork)

# Load necessary data: abundance data and metadata
abundance_file <- "abundance_file.tsv"
metadata <- read_delim(
    "metadata.txt",
    delim = "\t",
    escape_double = FALSE,
    trim_ws = TRUE
)

# Run ggpicrust2 with input file path
results_file_input <- ggpicrust2(file = abundance_file,
                                 metadata = metadata,
                                 group = "State", # For example dataset, group = "Environment"
                                 pathway = "MetaCyc",
                                 daa_method = "LinDA",
                                 ko_to_kegg = FALSE,
                                 order = "State",
                                 p_values_bar = TRUE,
                                 x_lab = "pathaway_name")
ggpicrust2 Rstudio PICRUSt2 • 109 views
ADD COMMENT

Login before adding your answer.

Traffic: 4424 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6