pathway_errorbar no longer working to graph data

[AbbiHern]

Describe the Bug
I am trying to re-graph a portion of my code that used to work flawlessly, but am now getting all sorts of errors.

Reproducible Example
Here is the code for the figure (note ec_abundance is the abundance file I imported and "daa_annotated_sub_method_LinDA_results_df_filtered" is the dataframe with the top 25 most differentially abundant results.)

daa_annotated_sub_method_LinDA_results_df_filtered.txt
ec_abundance.csv
Long Term Keto Microbiome Metadata TRF Only.txt

pathway_errorbar(
    abundance = ec_abundance,
    daa_results_df = daa_annotated_sub_method_LinDA_results_df_filtered,
    Group = metadata$diet,
    p_values_threshold = 0.05,
    order = "name",
    select = NULL,
    ko_to_kegg = FALSE,
    p_value_bar = TRUE
  )

Expected Behavior
I expected to get the graphical output

Actual Behavior
I get the following error:

The 'method' column in the 'daa_results_df' data frame contains more than one method. Please filter it to contain only one method.
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 pathway_errorbar(abundance = ec_abundance, daa_results_df = daa_annotated_sub_method_LinDA_results_df_filtered, :
Visualization with 'pathway_errorbar' cannot be performed because there are no features with statistical significance. For possible solutions, please check the FAQ section of the tutorial.

Environment Information:

• Operating System: PC
• R Version: 4.1.2
• Package Version: 1.7.3

[cafferychen777]

Hi @AbbiHern,

Thank you for your patience, AbbiHern. I've realized that your issue is actually a common one that we've addressed in our GitHub repository. I'd like to direct you to a specific resource that should be very helpful in resolving your problem.

Please take a look at Issue 7 in our GitHub FAQ:
https://github.com/cafferychen777/ggpicrust2#issue-7-there-are-no-statistically-significant-biomarkers

This issue directly addresses the error message you received: "Visualization with 'pathway_errorbar' cannot be performed because there are no features with statistical significance."

The FAQ provides several possible reasons why you might not be finding statistically significant biomarkers:

1. The true difference between your groups might be small or non-existent.
2. Your sample size might be too small to detect the differences.
3. The variation within your groups might be too large.

It also offers some helpful suggestions:

1. Increase your sample size if possible to improve statistical power.
2. Look for ways to decrease intra-group variation, such as identifying outliers or subgroups.
3. Consider changing your statistical method or adjusting parameters.

Remember, not finding significant results is also a valid outcome. It might indicate that there are no substantial differences between the groups you're studying.

I encourage you to read through this FAQ entry carefully. It should provide you with some strategies to address your current issue and create a more informative visualization.

If you've tried these suggestions and are still facing difficulties, please don't hesitate to come back with more details about your data and analysis. We're here to help!

Best,