Fix vignette images

wejlab · Oct 5, 2024 · 7c4b588 · 7c4b588
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Showing 3 changed files with 3 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: LegATo
 Title: LegATo: Longitudinal mEtaGenomic Analysis Toolkit
-Version: 0.99.10
+Version: 0.99.11
 Authors@R: c(
     person("Aubrey", "Odom", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7113-7598")),

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -29,6 +29,7 @@ reference:
     - create_formatted_MAE
     - clean_MAE
     - filter_MAE
+    - filter_animalcules_MAE
   - title: "Reformat a MAE Object into a Data Frame"
     desc: "Take a animalcules-formatted MAE and reformat for visualizationa and analysis."
     contents:

diff --git a/vignettes/LegATo_vignette.Rmd b/vignettes/LegATo_vignette.Rmd
@@ -416,12 +416,7 @@ output <- run_gee_model(dat_1, unit_var = "Subject",
               plot_terms = "timepoint",
               width = 6, height = 4, units = "in", scale = 0.7)
 
-list.files(tempfolder)
-
-knitr::include_graphics(file.path(tempfolder, "Dolosigranulum_timepoint.png"))
-knitr::include_graphics(file.path(tempfolder, "Streptococcus_timepoint.png"))
-
-unlink(tempfolder, recursive = TRUE)
+list.files(tempfolder) |> head()
 ```
 
 ### Linear Mixed Models