topr plot functions

Examples of basic usage. For more examples on how to use each plot function select the function name from the top navigation bar.

library(topr)

manhattan

Single GWAS

manhattan(CD_UKBB, annotate=5e-9)

Multi GWAS

manhattan(list(CD_UKBB, CD_FINNGEN), annotate=5e-9)
[1] "Use the legend_labels argument to change the legend labels from color names to meaningful labels! "

See manhattan for more examples and common use cases.

regionplot

Single GWAS

regionplot(CD_UKBB, gene="IL23R", annotate=5e-9)
Warning: 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 topr package.
  Please report the issue at <https://github.com/totajuliusd/topr/issues>.
[1] "Zoomed to region:  1:67038907-67359979"

Multi GWAS

regionplot(list(CD_UKBB, CD_FINNGEN), gene="IL23R", annotate=5e-9)
[1] "Use the legend_labels argument to change the legend labels from color names to meaningful labels! "
[1] "Zoomed to region:  1:67038907-67359979"

See regionplot for more examples.

locuszoom

locuszoom(R2_CD_UKBB)
[1] "Zoomed to region:  1:67042284-67359988"

foresttopr

 primary_dat <- CD_UKBB |>
      dplyr::arrange(P) |>
      head(n = 10) |>
      annotate_with_nearest_gene()

foresttopr(
  dat = list(
    primary_dat,
    CD_FINNGEN
  ),
  key_col = "ID",
  label_col = "Gene_Symbol",
  legend_labels = c("CD_UKBB", "CD_FINNGEN"),
  effect_type = "beta"
)

See foresttopr for more examples and common use cases.

effectplot

effectplot(list(CD_UKBB, CD_FINNGEN), annotate=5e-4)

 effectplot(list(CD_FINNGEN, CD_UKBB), color = get_topr_colors()[2], annotate=5e-4)

Other species