Merge pull request #4 from oliviaAB/main

CRAN submission

.Rbuildignore

@@ -10,3 +10,5 @@
 ^\.github$
 ^README\.Rmd$
 ^README.html$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.github/workflows/pkgdown.yaml

@@ -30,7 +30,8 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, local::., github::jendelman/GWASpoly
+
           needs: website
 
       - name: Build site

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.1.0
+Date: 2023-02-09 02:07:37 UTC
+SHA: f009eb969d5eba81478b12f374e1547f7fd98bc4

DESCRIPTION

@@ -1,18 +1,19 @@
 Package: hidecan
-Title: Hidecan plots generator
-Version: 1.0.0
+Title: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results
+Version: 1.1.0
 Authors@R: 
     person("Olivia", "Angelin-Bonnet", , "olivia.angelin-bonnet@plantandfood.co.nz", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7708-2919"))
-Description: A package for generating hidecan plots that summarise and combine 
-  the results of GWAS and transcriptomics differential expression analyses,
-  along candidate genes of interest.
+Description: Generates HIDECAN plots that summarise and combine 
+  the results of genome-wide association studies (GWAS) and transcriptomics 
+  differential expression analyses (DE), along with manually curated candidate genes of interest. The HIDECAN plot 
+  is presented in Angelin-Bonnet et al. (2023) (currently in review).
 License: MIT + file LICENSE
-URL: https://shiny-adventure-acfe02d1.pages.github.io/, https://github.com/PlantandFoodResearch/hidecan
+URL: https://plantandfoodresearch.github.io/hidecan/, https://github.com/PlantandFoodResearch/hidecan
 BugReports: https://github.com/PlantandFoodResearch/hidecan/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 2.10)
 Imports: 
@@ -26,12 +27,11 @@ Imports:
     tidyr,
     viridis,
     vroom
-Suggests: 
-    GWASpoly,
+Suggests:
     knitr,
     rmarkdown,
     stringr,
     testthat (>= 3.0.0)
-Remotes: jendelman/GWASpoly
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Language: en-GB

NAMESPACE

@@ -17,7 +17,6 @@ export(combine_chrom_length)
 export(compute_chrom_length)
 export(create_hidecan_plot)
 export(get_example_data)
-export(get_gwaspoly_example_data)
 export(hidecan_plot)
 export(hidecan_plot_from_gwaspoly)
 export(run_hidecan_shiny)

NEWS.md

@@ -0,0 +1,5 @@
+# hidecan 1.1.0
+
+* Removed `get_gwaspoly_example_data()` function so that the package doesn't depend on GWASpoly (for CRAN submission)
+
+* Saved the example object previously returned by `get_gwaspoly_example_data()` in as an `rda` file in the `extdata` folder

R/create_hidecan_plot.R

@@ -38,9 +38,9 @@
 #' @param label_padding Numeric, amount of padding around gene labels in the plot,
 #' as unit or number. Default value is 0.15
 #' (for \link[ggrepel]{geom_label_repel}).
-#' @returns A ggplot.
+#' @returns A `ggplot`.
 #' @examples
-#' \dontrun{
+#' if (interactive()) {
 #' x <- get_example_data()
 #' y <- list("GWAS" = GWAS_data(x[["GWAS"]]),
 #'           "DE" = DE_data(x[["DE"]]),
@@ -387,9 +387,9 @@ create_hidecan_plot <- function(x,
 #' giving for each chromosome its length in bp. If `NULL` (the default), will
 #' be inferred from the GWAS, DE and candidate gene data.
 #' @inheritParams create_hidecan_plot
-#' @returns a ggplot.
+#' @returns a `ggplot`.
 #' @examples
-#' \dontrun{
+#' if (interactive()) {
 #' x <- get_example_data()
 #'
 #' ## Typical example with one GWAs result table, one DE result table and

R/gwaspoly_helper_functions.R

@@ -1,6 +1,6 @@
 #' Extracts information from GWASpoly output
 #'
-#' Extracts GWAS results and chomosome length from GWASpoly output.
+#' Extracts GWAS results and chromosome length from GWASpoly output.
 #'
 #' @param gwaspoly_output A `GWASpoly.fitted` or `GWASpoly.thresh` object
 #' (returned by `GWASpoly::GWASpoly()` or `GWASpoly::set.threshold()` functions).
@@ -127,13 +127,7 @@ GWAS_data_from_gwaspoly <- function(gwaspoly_output,
 #' @inheritParams GWAS_data_from_gwaspoly
 #' @param ... Further arguments passed to the \code{\link{create_hidecan_plot}()}
 #' function.
-#' @returns A ggplot.
-#' @examples
-#' \dontrun{
-#' x <- get_gwaspoly_example_data(with_thresholds = TRUE)
-#'
-#' hidecan_plot_from_gwaspoly(x)
-#' }
+#' @returns A `ggplot`.
 #' @export
 hidecan_plot_from_gwaspoly <- function(gwaspoly_output,
                                        traits = NULL,

R/shiny_app.R

@@ -3,9 +3,16 @@
 #' Starts the HIDECAN shiny app. The app reads in csv data to produce
 #' a HIDECAN plot.
 #'
+#' @returns No return value, called for side effects (launching the shiny app).
+#'
 #' @export
 run_hidecan_shiny <- function(){
   app_dir <- system.file("shiny_apps/hidecan_shiny.R", package = "hidecan")
 
   shiny::runApp(app_dir, display.mode = "normal")
 }
+
+## To get rid of the check NOTE
+ignore_unused_imports <- function(){
+  vroom::vroom
+}

R/utils.R

@@ -35,22 +35,26 @@ get_example_data <- function(){
   )
 }
 
-#' GWASpoly example dataset
-#'
-#' Returns a list of GWASpoly example datasets.
-#'
-#' @param with_thresholds Logical, should the GWASpoly object returned
-#' contain significance threshold? Default value is `TRUE`.
-#' @returns
-#' * if `with_thresholds` is `TRUE`: a `GWASpoly.thresh` object
-#' (returned by the `GWASpoly::set.threshold()` function).
-#' if `with_thresholds` is `FALSE`: a `GWASpoly.fitted` object
-#' (returned by the `GWASpoly::GWASpoly()` function).
-#' @export
-get_gwaspoly_example_data <- function(with_thresholds = TRUE){
-  if(with_thresholds){
-    return(gwaspoly_res_thr)
-  } else {
-    return(gwaspoly_res)
-  }
-}
+# #' GWASpoly example dataset
+# #'
+# #' Returns a list of GWASpoly example datasets. Not exported because otherwise
+# #' would load the GWASpoly package which is not on CRAN.
+# #'
+# #' Install the GWASpoly package with `devtools::install_github('jendelman/GWASpoly', build_vignettes=FALSE)`.
+# #'
+# #' @param with_thresholds Logical, should the GWASpoly object returned
+# #' contain significance threshold? Default value is `TRUE`.
+# #' @returns
+# #' * if `with_thresholds` is `TRUE`: a `GWASpoly.thresh` object
+# #' (returned by the `GWASpoly::set.threshold()` function).
+# #' if `with_thresholds` is `FALSE`: a `GWASpoly.fitted` object
+# #' (returned by the `GWASpoly::GWASpoly()` function).
+# #' @export
+# get_gwaspoly_example_data <- function(with_thresholds = TRUE){
+#
+#   if(with_thresholds){
+#     return(gwaspoly_res_thr)
+#   } else {
+#     return(gwaspoly_res)
+#   }
+# }

_pkgdown.yml

@@ -13,9 +13,9 @@ navbar:
       - text: Step-by-step
         href: articles/hidecan-step-by-step.html
       - text: GWASpoly output
-        href: articles/gwaspoly_output.html
+        href: articles/web_only/gwaspoly_output.html
       - text: Shiny app
-        href: articles/shiny-app.html
+        href: articles/web_only/shiny-app.html
 
 home:
   sidebar:
@@ -58,7 +58,6 @@ reference:
 - title: "Example datasets"
   contents:
   - get_example_data
-  - get_gwaspoly_example_data
 
 - title: "Utils"
   contents:

cran-comments.md

@@ -0,0 +1,47 @@
+# Resubmission
+
+This is a resubmission. In this version I have:
+
+* Explained acronyms in the description of the package.
+
+* Added the missing \value tag in the run_hidecan_shiny.Rd documentation.s
+
+# Test environments
+
+- local Windows 10, R 4.2.2
+- Winbuilder: x86_64-w64-mingw32 (64-bit) R version 4.2.2 (2022-10-31 ucrt)
+- Winbuilder: x86_64-w64-mingw32 (64-bit) R Under development (unstable) (2023-01-25 r83685 ucrt)
+- Rhub:
+  - Windows Server 2022, R-devel, 64 bit
+  - Fedora Linux, R-devel, clang gfortran
+  - Ubuntu Linux 20.04 LTS, R-release, GCC
+  - macOS 10.13.6 High Sierra, R-release, brew
+  - debian-gcc-release: Debian Linux, R-release, GCC
+
+# R CMD check results
+
+There were no ERRORs, WARNINGs. 
+
+There was 1 NOTE:
+
+```
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: 'Olivia Angelin-Bonnet <olivia.angelin-bonnet@plantandfood.co.nz>'
+
+New submission
+
+Possibly misspelled words in DESCRIPTION:
+  Angelin (11:19)
+  GWAS (9:51)
+  HIDECAN (2:15, 8:24, 10:103)
+  al (11:37)
+  et (11:34)
+  transcriptomics (9:61)
+```
+
+This is a new submission. Angelin is a family name; GWAS stands for Genome-Wide Association Study (precised in the description); HIDECAN is the name of the package; transcriptomics is correctly spelled; et al. was used for a reference.
+
+
+# Downstream dependencies
+
+There are currently no downstream dependencies for this package.

data-raw/datasets_for_tests.R

@@ -10,3 +10,40 @@ can_res <- hidecan::CAN_data(candidate_data)
 
 save(gwas_res, de_res, can_res, file = "tests/testthat/data-test/test_input.rda")
 
+
+library(GWASpoly)
+library(readr)
+library(dplyr)
+
+genofile <- system.file("extdata", "TableS1.csv", package = "GWASpoly")
+phenofile <- system.file("extdata", "TableS2.csv", package = "GWASpoly")
+
+set.seed(10)
+geno_data <- read_csv(genofile) |>
+  slice_sample(n = 500)
+
+temp_file <- tempfile()
+write_csv(geno_data, temp_file)
+
+data <- read.GWASpoly(ploidy = 4,
+                      pheno.file = phenofile,
+                      geno.file = temp_file,
+                      format = "ACGT",
+                      n.traits = 13,
+                      delim = ",")
+
+data.original <- set.K(data,
+                       LOCO = FALSE,
+                       n.core = 2)
+
+
+gwaspoly_res <- GWASpoly(data.original,
+                         models = c("general", "additive"),
+                         traits = c("tuber_eye_depth", "tuber_shape"),
+                         n.core = 2)
+
+gwaspoly_res_thr <- set.threshold(gwaspoly_res, method = "M.eff", level = 0.05)
+
+## For users to access the example GWASpoly dataset without having it loaded
+saveRDS(gwaspoly_res, file = "tests/testthat/data-test/test_gwaspoly_res.rda")
+saveRDS(gwaspoly_res_thr, file = "tests/testthat/data-test/test_gwaspoly_res_thr.rda")

data-raw/making_example_data.R

@@ -86,11 +86,57 @@ gwaspoly_res <- GWASpoly(data.original,
 
 gwaspoly_res_thr <- set.threshold(gwaspoly_res, method = "M.eff", level = 0.05)
 
+## For users to access the example GWASpoly dataset without having it loaded
+saveRDS(gwaspoly_res_thr, file = "inst/extdata/gwaspoly_res_thr.rda")
+
 #manhattan.plot(gwaspoly_res_thr)
 
 
 ## ----------------- ##
 ## Saving everything ##
 ## ----------------- ##
 
-usethis::use_data(gwas_data, de_data, candidate_data, gwaspoly_res, gwaspoly_res_thr, internal = TRUE, overwrite = TRUE)
+## To reduce the size of the dataset, removing at random some of the non-significant
+## markers and genes
+
+## Preserving the end of each chromosome
+gwas_data_ends <- gwas_data |>
+  group_by(chromosome) |>
+  slice_max(position, n = 1) |>
+  ungroup()
+
+de_data_ends <- de_data |>
+  group_by(chromosome) |>
+  slice_max(end, n = 1) |>
+  ungroup()
+
+## Keeping the significant markers/genes
+gwas_data_sign <- gwas_data |>
+  filter(score >= 3.5)
+
+de_data_sign <- de_data |>
+  filter(padj <= 0.05)
+
+## Randomly subsetting non-significant markers/genes
+gwas_data_subset <- gwas_data |>
+  filter(score < 3.5) |>
+  slice_sample(prop = 0.5)
+
+de_data_subset <- de_data |>
+  filter(padj > 0.05) |>
+  slice_sample(prop = 0.5)
+
+## Combining retained markers/genes
+gwas_data <- bind_rows(
+  gwas_data_ends,
+  gwas_data_sign,
+  gwas_data_subset
+)
+
+de_data <- bind_rows(
+  de_data_ends,
+  de_data_sign,
+  de_data_subset
+)
+
+usethis::use_data(gwas_data, de_data, candidate_data, internal = TRUE, overwrite = TRUE)