Error in `dplyr::mutate()`

Question

[shamza]

Hey all, I am trying to run this script in R but due to some reason I am getting the following error, I don't know what I am missing. Any help would be appreciated.

library("tidyverse")
library("ggrepel")
library("dplyr")

df |>
  dplyr::mutate(
    label=ifelse(
      avg_log2FC >= nth(avg_log2FC, 10, desc(avg_log2FC)) | avg_logFC <= nth(avg_log2FC, 10, avg_log2FC),
      Gene, NA),
    DEGs=dense_rank(-avg_log2FC)) |>
  ggplot(aes(x=DEGs, y=avg_log2FC)) +
  geom_point(aes(color=avg_log2FC), show.legend=FALSE) +
  geom_text_repel(aes(label=label)) +
  geom_hline(yintercept=0, linetype="dashed")

I am trying to construct a visualization, a p-fold plot. This is what my df looks like and the plot I want to construct

gene         p_val avg_log2FC pct.1 pct.2     p_val_adj
RPS12         RPS12 1.806317e-144  0.7350248 1.000 0.991 2.477183e-140
RPS6           RPS6 7.135900e-142  0.6798622 1.000 0.995 9.786173e-138
RPS27         RPS27 5.257820e-140  0.7207819 0.999 0.992 7.210575e-136
RPL32         RPL32 4.229582e-136  0.6115515 0.999 0.995 5.800448e-132
RPS14         RPS14 1.799019e-130  0.6199183 1.000 0.994 2.467175e-126
RPS25         RPS25 5.507298e-123  0.7442491 0.997 0.975 7.552709e-119
RPS3           RPS3 1.412450e-117  0.6094866 1.000 0.994 1.937034e-113
RPL9           RPL9 3.657623e-117  0.7443112 0.994 0.971 5.016065e-113
RPL13         RPL13 7.368767e-117  0.5651751 1.000 0.996 1.010553e-112
RPL31         RPL31 2.746961e-116  0.7396594 0.996 0.964 3.767182e-112
RPL3           RPL3 6.398782e-113  0.6090295 0.997 0.995 8.775289e-109
RPL21         RPL21 3.609756e-111  0.6704414 0.997 0.991 4.950419e-107

Error in `dplyr::mutate()`:
  In argument: `label = ifelse(...)`.
Caused by error:
! unable to find an inherited method for function 'desc' for signature '"numeric"'
Run `rlang::last_trace()` to see where the error occurred.

Answer 1

[rpolicastro]

R might be using the wrong desc function. Try replacing it with dplyr::desc to explicitly call the function from the dplyr library.

[shamza]

it worked, Thank you!

[MH]

Can you provide the code to get similar color plot? Thank you