plot_locus fails due to deprecated ggplot2 syntax (`aes_string()`, `size` aesthetic)

[bingxunli]

I'm using R 4.5.1 with the latest version of ggplot2. The function plot_locus from the echoplot package fails because it relies on ggplot2 features that are now deprecated/defunct.

The specific errors/warnings I see:

• Error: invalid non-character version specification 'x' (type: double)
• aes_string() was deprecated in ggplot2 3.0.0.
• Using size aesthetic for lines was deprecated in ggplot2 3.4.0.

It seems the package needs to update to use aes() with tidy evaluation instead of aes_string(), and use linewidth instead of size for lines.

dat <- echodata::BST1
LD_matrix <- echodata::BST1_LD_matrix
locus_dir <- file.path(tempdir(), echodata::locus_dir)
plt <- tryCatch(

• echoplot::plot_locus(
  

•     dat = dat,
  

•     locus_dir = locus_dir,
  

•     LD_matrix = LD_matrix,
  

•     show_plot = FALSE,
  

•     save_plot = FALSE,
  

•     verbose = FALSE
  

• ),
  

• error = function(e) { message("plot_locus error: ", e$message); NULL }
  

• )
• support_thresh = 2
• Calculating mean Posterior Probability (mean.PP)...
• 4 fine-mapping methods used.
• 7 Credible Set SNPs identified.
• 3 Consensus SNPs identified.
• Filling NAs in CS cols with 0.
• Filling NAs in PP cols with 0.
  plot_locus error: The facets argument of facet_grid() was deprecated in ggplot2 2.2.0 and is now defunct.Please use the rows argument instead.
  warning:
  1: aes_string() was deprecated in ggplot2 3.0.0.
  ℹ Please use tidy evaluation idioms with aes().
  ℹ See also vignette("ggplot2-in-packages") for more information.
  ℹ The deprecated feature was likely used in the echoplot package.
  Please report the issue at https://github.com/RajLabMSSM/echoplot/issues.
  This warning is displayed once per session.
  Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
  2: Using size aesthetic for lines was deprecated in ggplot2 3.4.0.
  ℹ Please use linewidth instead.
  ℹ The deprecated feature was likely used in the echoplot package.
  Please report the issue at https://github.com/RajLabMSSM/echoplot/issues.
  This warning is displayed once per session.
  Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.

lifecycle::last_lifecycle_warnings()
[[1]]
<warning/lifecycle_warning_deprecated>
Warning:
aes_string() was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with aes().
ℹ See also vignette("ggplot2-in-packages") for more information.
ℹ The deprecated feature was likely used in the echoplot package.
Please report the issue at https://github.com/RajLabMSSM/echoplot/issues.

---

I think this is because package uses deprecated ggplot2 syntax (aes_string() and the size aesthetic for lines), which causes errors in recent R/ggplot2 versions. Please update to aes() + .data[[ ]] and linewidth
Could you please update the package to be compatible with recent ggplot2 versions? Thank you for your work on this package!