pathway_errorbar(): color was not mapped on the road when saving

[kestlermai]

Hello @cafferychen777, I used the ggsave function to save the pathway_errorbar in pdf format, and found that the color was not mapped on the road, but was saved in png format, so the color could normally mapp in the road. What's the problem? Code： library(ggpicrust2) library(tidyverse) library(GGally) library(ggprism) library(patchwork) library(ggh4x) data("ko_abundance") data("metadata") kegg_abundance <- ko2kegg_abundance(data = ko_abundance) daa_results_df <- pathway_daa(kegg_abundance, metadata = metadata, group = "Environment", daa_method = "LinDA") daa_annotated_results_df <- pathway_annotation(pathway = "KO", daa_results_df = daa_results_df, ko_to_kegg = TRUE) pathway_errorbar(abundance = kegg_abundance, daa_results_df = daa_annotated_results_df, Group = metadata$Environment, ko_to_kegg = TRUE, p_values_threshold = 0.05, order = "pathway_class", select = NULL, p_value_bar = TRUE, colors = NULL, x_lab = "pathway_name") ggsave(filename = "pathway_errobar1.pdf", width = 35, height = 15, units = "cm", dpi = 600) ggsave(filename = "pathway_errobar1.png", width = 35, height = 15, units = "cm", dpi = 600)

pathway_errobar1.pdf

[cafferychen777]

Hello @kestlermai,

Thank you for sharing the details. I'm not quite clear on what you mean by "the color was not mapped on the road". Could you please elaborate on this issue a bit more or possibly share a visual comparison between the PNG and PDF outputs? This will help me better understand the problem and provide a potential solution.

Best regards,

Chen YANG

[kestlermai]

Thank you for your reply, maybe I'm not clear enough. My question is as follows：

When I used the ggsave function to save the pathway_errorbar in png format, like in the picture below: the color is displayed normally. ggsave(filename = "pathway_errobar1.png", width = 35, height = 15, units = "cm", dpi = 600)

When I used the ggsave function to save the pathway_errorbar in pdf format, as shown in the figure below: ggsave(filename = "pathway_errobar1.pdf", width = 35, height = 15, units = "cm", dpi = 600)

[cafferychen777]

Hello @kestlermai ,

Thank you for providing more details. I used the same code on my end and the output appears normal for both PNG and PDF formats. It's possible that the issue might be related to your R version or even something specific to your computer. I recommend trying on a different computer or updating your R version to see if it resolves the issue.

Best regards,

Chen YANG

[kestlermai]

Thank you very much for your reply, I fixed this problem after updating my R version