fc.method = "compare_mean" can run but fc.method = "compare_median" can't run

[shaodongyan]

mpse1 %>% mp_cal_abundance(.abundance=Abundance, force=TRUE, relative=FALSE) %>% mp_diff_analysis(.abundance=Abundance, force=TRUE, relative=FALSE, .group=group, filter.p="pvalue",p.adjust = "BH",fc.method = "compare_median")

can't run . mpse1 %>%

• mp_cal_abundance(.abundance=Abundance, force=TRUE, relative=FALSE) %>%
• mp_diff_analysis(.abundance=Abundance, force=TRUE, relative=FALSE, .group=group, filter.p="pvalue",p.adjust = "BH",fc.method = "compare_mean") can . Thanks,But I don't konw Why

[shaodongyan]

and why is 1000%?

[xiangpin]

mp_diff_analysis(.abundance=Abundance, force=TRUE, relative=FALSE means the Abundance (may be count in your data) not relative abundance will be test.

[shaodongyan]

mp_diff_analysis(.abundance=Abundance, force=TRUE, relative=FALSE means the Abundance (may be count in your data) not relative abundance will be test.

My data is metaphlan3 data .The Abundance is relative abundance,So I don;t think it is the reason why "fc.method = "compare_median" " can't make sense. Thank you, xiangpin. Could you tell me why? Thanks

[xiangpin]

Please provide more information, I can not debug for you because you do not provide the reproducible analysis codes and data set. But, first please check the Abundance of mpse1 is relative abundance. You can just use compare_mean to identify which abundance of group is more. The compare_median will be deprecated in the next version.

mpse1 %>% mp_extract_assays(.abundance=Abundance) %>% colSums() %>% head()

[shaodongyan]

Please provide more information, I can not debug for you because you do not provide the reproducible analysis codes and data set. But, first please check the Abundance of mpse1 is relative abundance. You can just use compare_mean to identify which abundance of group is more. The compare_median will be deprecated in the next version.

mpse1 %>% mp_extract_assays(.abundance=Abundance) %>% colSums() %>% head()

C8-7d_remove_host_profile C8-77d_remove_host_profile C8-26d_remove_host_profile C8-175d_remove_host_profile 100.00001 100.00000 100.00001 99.93213 C8-140d_remove_host_profile C8-11d_remove_host_profile 99.91116 100.00000
Thank you! If The compare_median will be deprecated in the next version , I will use the deafult method. How I use the ggdiffbox() function in MPSE object? or how can i use other function to plot the similar plot such as ggdiffbox()? Thanks!

[xiangpin]

or how can i use other function to plot the similar plot such as ggdiffbox()?

You can use the mp_plot_diff_boxplot of github version (remotes::install_github('YuLab-SMU/MicrobiotaProcess')) to do it

refer to the following codes

library(MicrobiotaProcess)
data(mouse.time.mpse)
mouse.time.mpse %<>%
  mp_rrarefy()
mouse.time.mpse
mouse.time.mpse %<>%
   mp_diff_analysis(.abundance=RareAbundance,
                   .group=time,
                   first.test.alpha=0.01,
                   action="add")
library(ggplot2)
p1 <- mouse.time.mpse %>%
          mp_plot_diff_boxplot(.group = time) %>%
          set_diff_boxplot_color(
           values = c("deepskyblue", "orange"),
           guide = guide_legend(title=NULL)
         )

p2 <- mouse.time.mpse %>%
         mp_plot_diff_boxplot(
           taxa.class = c(Genus, OTU),
           group.abun = TRUE,
           removeUnknown = TRUE,
         ) %>%
         set_diff_boxplot_color(
           values = c("deepskyblue", "orange"),
           guide = guide_legend(title=NULL)
         )

aplot::plot_list(p1, p2)

[shaodongyan]

or how can i use other function to plot the similar plot such as ggdiffbox()?

You can use the mp_plot_diff_boxplot of github version (remotes::install_github('YuLab-SMU/MicrobiotaProcess')) to do it

refer to the following codes

library(MicrobiotaProcess)
data(mouse.time.mpse)
mouse.time.mpse %<>%
  mp_rrarefy()
mouse.time.mpse
mouse.time.mpse %<>%
   mp_diff_analysis(.abundance=RareAbundance,
                   .group=time,
                   first.test.alpha=0.01,
                   action="add")
library(ggplot2)
p1 <- mouse.time.mpse %>%
          mp_plot_diff_boxplot(.group = time) %>%
          set_diff_boxplot_color(
           values = c("deepskyblue", "orange"),
           guide = guide_legend(title=NULL)
         )

p2 <- mouse.time.mpse %>%
         mp_plot_diff_boxplot(
           taxa.class = c(Genus, OTU),
           group.abun = TRUE,
           removeUnknown = TRUE,
         ) %>%
         set_diff_boxplot_color(
           values = c("deepskyblue", "orange"),
           guide = guide_legend(title=NULL)
         )

aplot::plot_list(p1, p2)

Thanks! It works,But How can I get the raw data of mp_plot_diff_boxplot()?