version 0.0.9.9100

tidying up for next release

.github/SUPPORT.md

@@ -1,10 +1,12 @@
 # Getting help
 
+Thank you for using `{mgi.report.reader}`!
+
 - If you have a GitHub account, please
 [file an issue](https://github.com/patterninstitute/mgi.report.reader/issues/new)
 with your question or bug report.
 
-- If you do not have a GitHub account, you can contact the maintainer of this
+- If you do not have a GitHub account, you can contact Ramiro Magno, the maintainer of this
 package at <[email protected]>.
 
 - If your question pertains more directly to data obtained from the Mouse Genomics Informatics (MGI),

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mgi.report.reader
 Title: Read Mouse Genome Informatics Reports
-Version: 0.0.9.9000
+Version: 0.0.9.9100
 Authors@R: c(
     person("Ramiro", "Magno", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5226-3441")),

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(chromosomes)
-export(open_in_mgi)
+export(feature_types)
+export(marker_types)
+export(open_marker_in_mgi)
 export(read_report)
-export(report_datetime)
 export(report_file)
+export(report_last_modified)
 export(report_name)
 export(report_source)
 export(report_type)

R/browser.R

@@ -37,7 +37,7 @@ mgi_reports_index_md <- function() {
 
 #' Browse MGI markers online
 #'
-#' [open_in_mgi()] launches the web browser and opens a tab for each MGI
+#' [open_marker_in_mgi()] launches the web browser and opens a tab for each MGI
 #' accession identifier on the Mouse Genome Informatics web interface:
 #' \url{https://www.informatics.jax.org}.
 #'
@@ -48,14 +48,14 @@ mgi_reports_index_md <- function() {
 #'
 #' @examples
 #' # Read about Acta1 (actin alpha 1, skeletal muscle) online.
-#' open_in_mgi("MGI:87902")
+#' open_marker_in_mgi("MGI:87902")
 #'
-#' # `open_in_mgi()` is vectorized, so you can open multiple pages.
+#' # `open_marker_in_mgi()` is vectorized, so you can open multiple pages.
 #' # NB: think twice if you really need to open many tabs at once.
-#' open_in_mgi(c("MGI:87902", "MGI:87909"))
+#' open_marker_in_mgi(c("MGI:87902", "MGI:87909"))
 #'
 #' @export
-open_in_mgi <- function(marker_id) {
+open_marker_in_mgi <- function(marker_id) {
   if (!(all(is_mgi_identifier(marker_id))))
     stop("`marker_id` must be a character vector of valid MGI identifiers.")
 

R/data.R → R/feature_types.R

@@ -1,20 +1,36 @@
-#' Genome Feature Types
+#' Genome Feature Type Definitions
 #'
 #' A dataset containing different types of gene and genome features along with
 #' their Sequence Ontology (SO) identifiers and definitions.
 #'
-#' @format A [tibble][tibble::tibble-package] with `r nrow(feature_types)` rows
-#'   and `r ncol(feature_types)` variables:
+#' @format A [tibble][tibble::tibble-package] with `r nrow(feature_type_definitions)` rows
+#'   and `r ncol(feature_type_definitions)` variables:
 #' \describe{
 #'   \item{feature_type}{Character. The type of gene or genome feature.}
 #'   \item{so_id}{Character. The Sequence Ontology identifier associated with the feature type.}
 #'   \item{definition}{Character. The definition of the feature type.}
 #' }
 #'
 #' @examples
-#' print(feature_types, n = Inf)
+#' print(feature_type_definitions, n = Inf)
 #'
 #' @source
 #'   The table in \url{https://www.informatics.jax.org/userhelp/GENE_feature_types_help.shtml}
 #'   and a few other terms found in MGI reports.
-"feature_types"
+"feature_type_definitions"
+
+
+#' Genome Feature types
+#'
+#' [feature_types()] returns different types of gene and genome features. For
+#' feature type definitions, see `?feature_type_definitions`.
+#'
+#' @returns A character vector of feature types' names.
+#'
+#' @examples
+#' feature_types()
+#'
+#' @export
+feature_types <- function() {
+  feature_type_definitions$feature_type
+}

R/marker_types.R

@@ -1,3 +1,13 @@
+#' Genetic marker types
+#'
+#' [marker_types()] returns MGI marker types.
+#'
+#' @returns A character vector.
+#'
+#' @examples
+#' marker_types()
+#'
+#' @export
 marker_types <- function() {
   c(
     "Gene",

R/read_report.R

@@ -74,7 +74,7 @@ read_report <- function(report_key = NULL,
   rpt_last_modified <- find_report_last_modified(report_file)
 
   attr(tbl, "report_source") <- rpt_source
-  attr(tbl, "report_datetime") <- rpt_last_modified
+  attr(tbl, "report_last_modified") <- rpt_last_modified
 
   tbl
 }

R/report_column_processing.R

@@ -37,12 +37,12 @@
 #   factor(marker_type, levels = marker_types())
 # }
 
-protein_ids_col <- function(protein_ids) {
-
-  protein_ids <- strsplit(protein_ids, " ", fixed = TRUE)
-  # Convert single NA values to empty character vectors in the list-column.
-  dplyr::if_else(sapply(protein_ids, \(x) length(x) == 1L && is.na(x)), list(character()), protein_ids)
-}
+# protein_ids_col <- function(protein_ids) {
+#
+#   protein_ids <- strsplit(protein_ids, " ", fixed = TRUE)
+#   # Convert single NA values to empty character vectors in the list-column.
+#   dplyr::if_else(sapply(protein_ids, \(x) length(x) == 1L && is.na(x)), list(character()), protein_ids)
+# }
 
 # cell_line_col <- function(cell_line) {
 #
@@ -51,16 +51,16 @@ protein_ids_col <- function(protein_ids) {
 #   dplyr::if_else(sapply(cell_line, \(x) length(x) == 1L && is.na(x)), list(character()), cell_line)
 # }
 
-special_feature_type_col <- function(feature_type) {
-
-  # In cases like:
-  # "lncRNA gene|lncRNA gene|lncRNA gene"
-  # keep only one instance. This assumes the values pipe-separated are repeated,
-  # this is the case in MRK_ENSEMBL.rpt.
-  feature_type <- sub("\\|.+", "", feature_type)
-
-  factor(feature_type, levels = feature_types$feature_type)
-}
+# special_feature_type_col <- function(feature_type) {
+#
+#   # In cases like:
+#   # "lncRNA gene|lncRNA gene|lncRNA gene"
+#   # keep only one instance. This assumes the values pipe-separated are repeated,
+#   # this is the case in MRK_ENSEMBL.rpt.
+#   feature_type <- sub("\\|.+", "", feature_type)
+#
+#   factor(feature_type, levels = feature_types$feature_type)
+# }
 
 # biotype_col <- function(biotype) {
 #   biotype <- strsplit(biotype, "|", fixed = TRUE)

R/report_source.R

@@ -40,19 +40,25 @@ find_report_last_modified <- function(file) {
   NA_character_
 }
 
-#' Report datetime
+#' Report last modification date
 #'
-#' [report_datetime()] the last modified date and time of the report source
-#' (local file or remote file).
+#' [report_last_modified()] returns the last modified date and time of the
+#' report source (local file or remote file).
 #'
 #' @param tbl Report data as a [tibble][tibble::tibble-package].
 #'
 #' @returns A last modified date-time as a [POSIXct][base::DateTimeClasses]
 #'   object.
 #'
+#' @examples
+#' markers <- read_report("marker_list1", n_max = 10L)
+#'
+#' # When was the report file last updated?
+#' report_last_modified(markers)
+#'
 #' @export
-report_datetime <- function(tbl) {
-  attr(tbl, "report_datetime")
+report_last_modified <- function(tbl) {
+  attr(tbl, "report_last_modified")
 }
 
 
@@ -65,6 +71,12 @@ report_datetime <- function(tbl) {
 #'
 #' @returns A single string with an absolute path to a file on disk or an URL.
 #'
+#' @examples
+#' markers <- read_report("marker_list1", n_max = 10L)
+#'
+#' # Where did the data come from?
+#' report_source(markers)
+#'
 #' @export
 report_source <- function(tbl) {
   attr(tbl, "report_source")

R/reports.R

@@ -33,9 +33,9 @@ get_reports_col <- function(report_key, col) {
     dplyr::pull(col)
 }
 
-#' Get report attributes by report key
+#' Get MGI report specs by report key
 #'
-#' Set of functions to retrieve attributes of a MGI report.
+#' Set of functions to retrieve metadata details of a MGI report.
 #'
 #' @inheritParams common-args
 #'

R/variable_types.R

@@ -65,7 +65,7 @@ col_strand <- function(x) {
 }
 
 col_feature_type <- function(x) {
-  factor(x, levels = feature_types$feature_type) |>
+  factor(x, levels = feature_types()) |>
     add_label_to_feature_type()
 }
 

_pkgdown.yml

@@ -6,9 +6,14 @@ template:
 
 navbar:
   structure:
-    left:  [intro, articles, reference, news]
+    left:  [intro, concepts, articles, reference, news]
     right: [search, github]
   components:
+    concepts:
+      text: Concepts
+      menu:
+        - text: Genetic Marker
+          href: articles/genetic_marker.html
     articles:
       text: Reports
       menu:
@@ -45,20 +50,24 @@ navbar:
 reference:
 - title: MGI Reports
 
+- subtitle: Reading Reports
+  contents:
+  - read_report
+  - report_source
+  - report_last_modified
+  - report-attributes
+
 - subtitle: Data
   contents:
   - reports
-  - feature_types
+  - feature_type_definitions
 
-- subtitle: Reading
+- subtitle: Enumerations
   contents:
-  - read_report
-  - report_source
-  - report_datetime
+  - chromosomes
+  - marker_types
+  - feature_types
 
 - subtitle: Helpers
   contents:
-  - open_in_mgi
-  - chromosomes
-  - report-attributes
-
+  - open_marker_in_mgi

data-raw/data.R

@@ -97,15 +97,15 @@ order <-
     61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71
   )
 
-feature_types <- feature_types01[order, ]
+feature_type_definitions <- feature_types01[order, ]
 
 # Export to file too.
-readr::write_csv(feature_types, file = "data-raw/feature_types.csv")
+readr::write_csv(feature_type_definitions, file = "data-raw/feature_type_definitions.csv")
 readr::write_csv(reports, file = "data-raw/reports.csv")
 
 # Export data sets
-usethis::use_data(feature_types, overwrite = TRUE, compress = "xz")
+usethis::use_data(feature_type_definitions, overwrite = TRUE, compress = "xz")
 usethis::use_data(reports, overwrite = TRUE, compress = "xz")
 
 # Internal data
-usethis::use_data(reports, feature_types, internal = TRUE, overwrite = TRUE)
+usethis::use_data(reports, feature_type_definitions, internal = TRUE, overwrite = TRUE)