cafferychen777
commented
1 year ago Hi,
Thanks for using ggpicrust2 and for reaching out. Regarding the error message you received with the pathway_errorbar function, it seems that the error message "The feature with statistically significance is zero, pathway_errorbar can't do the visualization." means that there are no results in pa_results with p.adjust values less than 0.05. As a result, the function is unable to perform the visualization.
To resolve this issue, I suggest checking the pa_results dataframe to ensure that it contains the expected results with p.adjust values less than 0.05. If the results are not as expected, you may want to adjust the analysis parameters or thresholds to obtain the desired results.
Please let me know if you have any further questions or concerns.
Best, Chen YANG
andressamv @.***> 于2023年5月10日周三 06:37写道：
Hi (and thanks for creating this tool!)
I am running ggpicrust2 one function at a time but struggling with the pathway_errorbar function.
My code kegg_abundance <- ko2kegg_abundance(abundance_file)
daa_results <- pathway_daa(kegg_abundance, meta_table, 'Day', daa_method = 'ALDEx2', select = NULL, p.adjust = 'bonferroni', reference = NULL)
daa_results_method <- daa_results[daa_results$method == 'ALDEx2_Kruskal-Wallace test', ]
daa_results_method1 <- daa_results_method[1:100,] daa_results_method2 <- daa_results_method[101:200,] daa_results_method3 <- daa_results_method[201:253,]
pa_results1 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method1, ko_to_kegg = TRUE) pa_results2 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method2, ko_to_kegg = TRUE) pa_results3 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method3, ko_to_kegg = TRUE)
pa_results <- rbind(pa_results1, pa_results2, pa_results3)
pa_results_padj <- subset(pa_results, p_adjust < 0.001)
Group <- meta_table$Day
daa_results_list <- pathway_errorbar(abundance = kegg_abundance, daa_results_df = pa_results, Group = Group, ko_to_kegg = TRUE, p_values_threshold = 0.05, order = "pathway_class", select = 'NULL', p_value_bar = TRUE, colors = NULL, x_lab = 'description')
Output of pathway_errorbar The feature with statistically significance is zero, pathway_errorbar can't do the visualization. Error in h(simpleError(msg, call)) : error in evaluating the argument 'physeq' in selecting a method for function 'taxa_are_rows': invalid class “otu_table” object: OTU abundance data must have non-zero dimensions.
Can you please help me with this error? Everything else worked fine!
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andressamv
Hi (and thanks for creating this tool!)
I am running ggpicrust2 one function at a time but struggling with the pathway_errorbar function.
My code kegg_abundance <- ko2kegg_abundance(abundance_file)
daa_results <- pathway_daa(kegg_abundance, meta_table, 'Day', daa_method = 'ALDEx2', select = NULL, p.adjust = 'bonferroni', reference = NULL)
daa_results_method <- daa_results[daa_results$method == 'ALDEx2_Kruskal-Wallace test', ]
daa_results_method1 <- daa_results_method[1:100,] daa_results_method2 <- daa_results_method[101:200,] daa_results_method3 <- daa_results_method[201:253,]
pa_results1 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method1, ko_to_kegg = TRUE) pa_results2 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method2, ko_to_kegg = TRUE) pa_results3 <- pathway_annotation(pathway = 'KO', daa_results_df = daa_results_method3, ko_to_kegg = TRUE)
pa_results <- rbind(pa_results1, pa_results2, pa_results3)
pa_results_padj <- subset(pa_results, p_adjust < 0.001)
Group <- meta_table$Day
daa_results_list <- pathway_errorbar(abundance = kegg_abundance, daa_results_df = pa_results, Group = Group, ko_to_kegg = TRUE, p_values_threshold = 0.05, order = "pathway_class", select = 'NULL', p_value_bar = TRUE, colors = NULL, x_lab = 'description')
_Output of pathwayerrorbar The feature with statistically significance is zero, pathway_errorbar can't do the visualization. Error in h(simpleError(msg, call)) : error in evaluating the argument 'physeq' in selecting a method for function 'taxa_are_rows': invalid class “otu_table” object: OTU abundance data must have non-zero dimensions.
Can you please help me with this error? Everything else worked fine! My pa_results table doesn't have a column called x_lab. Is this the problem?