error in generating pathway_errorbar

[sierra-uga]

Set up metadata + abundance data

metadata <- metadata %>% filter(., Sample.Control == "True.Sample") %>% filter(., sample_name != "STN115.35.fil.dura.r1") # remove sample that isn't in KO abundance for some reason
outflow_metadata <- metadata %>% filter(., Transect_Name == "transect2") # filter by transect2

abundance_data <- read_delim(abundance_file, delim = "\t", col_names = TRUE, trim_ws = TRUE) # read in KO dataset
ColumnstoKeep <- c("#NAME", outflow_metadata$sample_name) # set vector of list of names to keep + KO Name column
KO_abundance_data <- subset(abundance_data, select = ColumnstoKeep) # subset (select columns) based on ColumnstoKeep

daa_results_df <- pathway_daa(abundance = KO_abundance_data %>% column_to_rownames("#NAME"), metadata = outflow_metadata, group = "Filter_pores", daa_method = "ALDEx2", select = NULL, reference = NULL)

# Filter results for ALDEx2_Kruskal-Wallace test method
daa_sub_method_results_df <- daa_results_df[daa_results_df$method == "ALDEx2_Kruskal-Wallace test", ]

daa_annotated_sub_method_results_df$group3 <- NULL # remove group 3 column for analysis

# Annotate pathway results without KO to KEGG conversion
daa_annotated_sub_method_results_df <- pathway_annotation(pathway = "KO", daa_results_df = daa_sub_method_results_df, ko_to_kegg = FALSE)

p <- pathway_errorbar(abundance = KO_abundance_data %>% column_to_rownames("#NAME"), daa_results_df = daa_annotated_sub_method_results_df, Group = outflow_metadata$Filter_type, p_values_threshold = 0.05, order = "group",
                      select = daa_annotated_sub_method_results_df %>% arrange(p_adjust) %>% slice(1:20) %>% dplyr::select(feature) %>% pull(), 
                      ko_to_kegg = FALSE, 
                      p_value_bar = TRUE, 
                      colors = NULL, 
                      x_lab = "description")

This happens successfully with no errors, until I try to view the pathway_errorbar...

> p 
Error in `guide_transform()`:
! <Guide> classes have been rewritten as <ggproto> classes.
The old S3 guide methods have been superseded.
Run `rlang::last_trace()` to see where the error occurred.

What is causing this error and how do I fix it?

Thank you so much!!
S

[cafferychen777]

Hello Sierra,

Thank you for reaching out and for using ggpicrust2. The error you're encountering with pathway_errorbar seems to be related to a recent change in the ggplot2 package. To resolve this, I recommend downgrading ggplot2 to version 3.4.0. You can do this by running the following command in R:

install.packages("ggplot2", version = "3.4.0", repos = "http://cran.us.r-project.org")

Please try this and let me know if it resolves the issue. I apologize for the inconvenience and appreciate your patience.

Best regards,
Chen YANG