cafferychen777
commented
7 months ago Hello,
Thank you for reaching out with your issue. To better assist you in resolving the problem, it would be very helpful if you could share your datasets with me. Having access to the actual data will allow me to replicate the error and provide a more accurate solution. If the datasets contain sensitive information, please ensure they are anonymized before sharing.
You can share the data by uploading it to a secure location and providing a download link, or if the datasets are not too large, you could also send them as email attachments. Please let me know the most convenient method for you.
Looking forward to your response so we can address this issue promptly.
Best regards, Chen YANG
saassli21
ivanllampy
cmetadea
mvirgilio
Hello @cafferychen777 , I have 2 datasets , I tested the script that is in #65 on the first and it worked nicely because when I print this command (daa_sub_method_results_df1 <- daa_results_df %>% filter(p_adjust < 0.05) %>% slice(1:29) ) I only have one group in group1 (P1) and group2 (CONTROL) . However when I tested the same script on my second dataset:
metadata <- read_delim("metadata_exp3.txt", delim = "\t", escape_double = FALSE, trim_ws = TRUE , comment = "#")
kegg_abundance <- ko2kegg_abundance("pred_metagenome_unstrat_exp3.tsv")
daa_results_df <- pathway_daa(abundance = kegg_abundance, metadata = metadata, group = "STATUS", daa_method = "LinDA", select = NULL, p.adjust = "BH" , reference = "T1")
daa_sub_method_results_df1 <- daa_results_df %>% filter(p_adjust < 0.05) %>% slice(1:29)
max(daa_sub_method_results_df1$p_adjust)
daa_annotated_sub_method_results_df1 <- pathway_annotation(pathway = "KO", daa_results_df = daa_sub_method_results_df1, ko_to_kegg = TRUE)
p <- pathway_errorbar(abundance = kegg_abundance, daa_results_df = daa_annotated_sub_method_results_df1, Group = metadata$STATUS, p_values_threshold = 0.05, order = "pathway_class", select = NULL, ko_to_kegg = TRUE, p_value_bar = TRUE, colors = NULL, x_lab = "pathway_name")
but I have this error : The 'group1' or 'group2' column in the 'daa_results_df' data frame contains more than one group. Please filter each to contain only one group.
Error in
levels<-(*tmp*, value = as.character(levels)) : factor level [5] is duplicatedthis error is due to the presence of multiple group in group1
I did this. does it correct ?
metadata <- read_delim("metadata_exp3.txt", delim = "\t", escape_double = FALSE, trim_ws = TRUE, comment = "#")
kegg_abundance <- ko2kegg_abundance("pred_metagenome_unstrat_exp3.tsv")
daa_results_df <- pathway_daa(abundance = kegg_abundance, metadata = metadata, group = "STATUS", daa_method = "LinDA", select = NULL, p.adjust = "BH", reference = "T1")
Get unique groups in 'group1'
unique_groups_group1 <- unique(daa_results_df$group1)
Initialize an empty list to store results
results_list <- list()
Iterate over each unique group
for (selected_group in unique_groups_group1) {
Filter the data for the current group
current_group_results <- daa_results_df %>% filter(group1 == selected_group)
Filter based on p_adjust and slice
filtered_slice <- current_group_results %>% filter(p_adjust < 0.05) %>% slice(1:29)
Annotate pathway results using KO to KEGG conversion
daa_annotated_results_df <- pathway_annotation(pathway = "KO", daa_results_df = filtered_slice, ko_to_kegg = TRUE)
Generate pathway error bar plot
p <- pathway_errorbar(abundance = kegg_abundance, daa_results_df = daa_annotated_results_df, Group = metadata$STATUS, p_values_threshold = 0.05, order = "pathway_class", select = NULL, ko_to_kegg = TRUE, p_value_bar = TRUE, colors = NULL, x_lab = "pathway_name")
Generate PCA plot
p1 <- pathway_pca(kegg_abundance, metadata, "STATUS")
Generate pathway heatmap
p2 <- pathway_heatmap(kegg_abundance %>% rownames_to_column("feature") %>% filter(feature %in% daa_annotated_results_df$feature) %>% column_to_rownames("feature"), metadata, "STATUS")
Save the plots to PNG files
ggsave(paste0("pathwayerrorbar", selected_group, ".png"), p, width = 30, height = 20, units = "in", dpi = 300) ggsave(paste0("pathwaypca", selected_group, ".png"), p1, width = 30, height = 20, units = "in", dpi = 300) ggsave(paste0("pathwayheatmap", selected_group, ".png"), p2, width = 30, height = 20, units = "in", dpi = 300)
Save the results in the list
results_list[[selected_group]] <- list(daa_annotated_results_df = daa_annotated_results_df, p = p, p1 = p1, p2 = p2) }