fix dotplot_pwys "bug" where it didn't reorder pwys

although pathways were usually already ordered by their combined p-values

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ezlimmaplot
 Title: Bioinformatics plots using limma and ggplot2, some from output of ezlimma
-Version: 0.0.2.9004
+Version: 0.0.3.9000
 Authors@R: c(person("Jonathan", "Dreyfuss", role = c("aut", "cre"), email = "[email protected]"),
              person("Hui", "Pan", role = "aut"),
 			 person("Grace", "Daher", role="ctb"))

R/dotplot_pwys.R

@@ -53,8 +53,8 @@ dotplot_pwys <- function(tab, prefix.v=NULL, name = NA, type.sig=c("p", "FDR"),
   # could do this in for loop separately for Mixed and not Mixed, but here I only need to do it once
   # then subset to 1st ntop rows: this does not cause error or warning even if ntop > nrow(ds)
   ds <- ds |> dplyr::arrange(!!rlang::sym(type.sig)) |>
-    dplyr::filter(!!rlang::sym(type.sig) < cut.sig) |>
-    dplyr::filter(Pwy %in% (ds |> dplyr::slice(1:ntop) |> dplyr::pull(Pwy)))
+    dplyr::filter(!!rlang::sym(type.sig) < cut.sig)
+  ds <- ds |> dplyr::filter(Pwy %in% (ds |> dplyr::slice(1:ntop) |> dplyr::pull(Pwy)))
   if (nrow(ds) == 0) stop("No pathways had ", type.sig, " < ", cut.sig, ".")
   pwy.max.nchar <- ds |> dplyr::pull(Pwy) |> nchar() |> max()
 

tests/testthat/test-dotplot_pwys.R

@@ -4,6 +4,10 @@ test_that("dotplot_pwy works", {
   expect_silent(dotplot_pwys(rc2, mixed="only", name="pwy"))
   rc.nomix <- rc2 |> dplyr::select(!contains("Mixed"))
   expect_silent(dotplot_pwys(rc.nomix, mixed="exclude", name="pwy"))
+  # make sure dotplot_pwys properly orders by p
+  res <- rc2 |> dplyr::arrange(desc(First3.p)) |>
+    dotplot_pwys(ntop=1)
+  expect_equal(unique(res$data$Pwy), "pwy1")
   unlink(x = "pwy_dotplot.pdf")
 
   expect_error(dotplot_pwys(rc2, name = NA, cut.sig = 10**-6))