From bbab104a04f12667e29426e9b829e806e80e92ac Mon Sep 17 00:00:00 2001
From: igor <6363505+igordot@users.noreply.github.com>
Date: Fri, 20 Dec 2024 23:22:19 -0500
Subject: [PATCH] Clean up code
---
.travis.yml | 14 ------
NAMESPACE | 12 -----
R/msigdbr.R | 43 +++++++++---------
R/utils-tidy-eval.R | 107 --------------------------------------------
man/tidyeval.Rd | 98 ----------------------------------------
5 files changed, 21 insertions(+), 253 deletions(-)
delete mode 100644 .travis.yml
delete mode 100644 R/utils-tidy-eval.R
delete mode 100644 man/tidyeval.Rd
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index a8280a0..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-language: r
-cache: packages
-
-r:
- - 3.3
- - oldrel
- - release
- - devel
-
-r_packages:
- - covr
-
-after_success:
- - Rscript -e 'library(covr); codecov()'
diff --git a/NAMESPACE b/NAMESPACE
index 0b77268..8e051f1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,6 @@
# Generated by roxygen2: do not edit by hand
export("%>%")
-export(":=")
-export(.data)
-export(as_label)
-export(as_name)
-export(enquo)
-export(enquos)
export(msigdbr)
export(msigdbr_collections)
export(msigdbr_show_species)
@@ -23,12 +17,6 @@ importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(magrittr,"%>%")
-importFrom(rlang,":=")
-importFrom(rlang,.data)
-importFrom(rlang,as_label)
-importFrom(rlang,as_name)
-importFrom(rlang,enquo)
-importFrom(rlang,enquos)
importFrom(tibble,as_tibble)
importFrom(tidyselect,any_of)
importFrom(tidyselect,everything)
diff --git a/R/msigdbr.R b/R/msigdbr.R
index 503e4cb..af5274a 100644
--- a/R/msigdbr.R
+++ b/R/msigdbr.R
@@ -28,7 +28,6 @@
#' msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
#' }
msigdbr <- function(species = "Homo sapiens", category = NULL, subcategory = NULL) {
-
# confirm that only one species is specified
if (length(species) > 1) {
stop("please specify only one species at a time")
@@ -62,11 +61,9 @@ msigdbr <- function(species = "Homo sapiens", category = NULL, subcategory = NUL
}
# combine gene sets and genes
- genesets_subset <-
- genesets_subset %>%
- inner_join(msigdbr_geneset_genes, by = "gs_id") %>%
- inner_join(msigdbr_genes, by = "gene_id") %>%
- select(-any_of(c("gene_id")))
+ genesets_subset <- inner_join(genesets_subset, msigdbr_geneset_genes, by = "gs_id")
+ genesets_subset <- inner_join(genesets_subset, msigdbr_genes, by = "gene_id", relationship = "many-to-many")
+ genesets_subset <- select(genesets_subset, !any_of(c("gene_id")))
# retrieve orthologs
if (species %in% c("Homo sapiens", "human")) {
@@ -82,7 +79,7 @@ msigdbr <- function(species = "Homo sapiens", category = NULL, subcategory = NUL
} else {
orthologs_subset <-
orthologs(genes = genesets_subset$human_ensembl_gene, species = species) %>%
- select(-any_of(c("human_symbol", "human_entrez"))) %>%
+ select(!any_of(c("human_symbol", "human_entrez"))) %>%
rename(
human_ensembl_gene = "human_ensembl",
gene_symbol = "symbol",
@@ -94,19 +91,21 @@ msigdbr <- function(species = "Homo sapiens", category = NULL, subcategory = NUL
}
# combine gene sets and orthologs
- genesets_subset %>%
- inner_join(orthologs_subset, by = "human_ensembl_gene") %>%
- arrange(.data$gs_name, .data$human_gene_symbol, .data$gene_symbol) %>%
- select(
- "gs_cat",
- "gs_subcat",
- "gs_name",
- "gene_symbol",
- "entrez_gene",
- "ensembl_gene",
- "human_gene_symbol",
- "human_entrez_gene",
- "human_ensembl_gene",
- everything()
- )
+ genesets_subset <- inner_join(genesets_subset, orthologs_subset, by = "human_ensembl_gene", relationship = "many-to-many")
+ genesets_subset <- arrange(genesets_subset, .data$gs_name, .data$human_gene_symbol, .data$gene_symbol)
+ genesets_subset <- select(
+ genesets_subset,
+ "gs_cat",
+ "gs_subcat",
+ "gs_name",
+ "gene_symbol",
+ "entrez_gene",
+ "ensembl_gene",
+ "human_gene_symbol",
+ "human_entrez_gene",
+ "human_ensembl_gene",
+ everything()
+ )
+
+ return(genesets_subset)
}
diff --git a/R/utils-tidy-eval.R b/R/utils-tidy-eval.R
deleted file mode 100644
index 09c3698..0000000
--- a/R/utils-tidy-eval.R
+++ /dev/null
@@ -1,107 +0,0 @@
-#' Tidy eval helpers
-#'
-#' @description
-#' This page lists the tidy eval tools reexported in this package from
-#' rlang. To learn about using tidy eval in scripts and packages at a
-#' high level, see the [dplyr programming
-#' vignette](https://dplyr.tidyverse.org/articles/programming.html)
-#' and the [ggplot2 in packages
-#' vignette](https://ggplot2.tidyverse.org/articles/ggplot2-in-packages.html).
-#' The [Metaprogramming
-#' section](https://adv-r.hadley.nz/metaprogramming.html) of [Advanced
-#' R](https://adv-r.hadley.nz) may also be useful for a deeper dive.
-#'
-#' * The tidy eval operators `{{`, `!!`, and `!!!` are syntactic
-#' constructs which are specially interpreted by tidy eval functions.
-#' You will mostly need `{{`, as `!!` and `!!!` are more advanced
-#' operators which you should not have to use in simple cases.
-#'
-#' The curly-curly operator `{{` allows you to tunnel data-variables
-#' passed from function arguments inside other tidy eval functions.
-#' `{{` is designed for individual arguments. To pass multiple
-#' arguments contained in dots, use `...` in the normal way.
-#'
-#' ```
-#' my_function <- function(data, var, ...) {
-#' data %>%
-#' group_by(...) %>%
-#' summarise(mean = mean({{ var }}))
-#' }
-#' ```
-#'
-#' * [enquo()] and [enquos()] delay the execution of one or several
-#' function arguments. The former returns a single expression, the
-#' latter returns a list of expressions. Once defused, expressions
-#' will no longer evaluate on their own. They must be injected back
-#' into an evaluation context with `!!` (for a single expression) and
-#' `!!!` (for a list of expressions).
-#'
-#' ```
-#' my_function <- function(data, var, ...) {
-#' # Defuse
-#' var <- enquo(var)
-#' dots <- enquos(...)
-#'
-#' # Inject
-#' data %>%
-#' group_by(!!!dots) %>%
-#' summarise(mean = mean(!!var))
-#' }
-#' ```
-#'
-#' In this simple case, the code is equivalent to the usage of `{{`
-#' and `...` above. Defusing with `enquo()` or `enquos()` is only
-#' needed in more complex cases, for instance if you need to inspect
-#' or modify the expressions in some way.
-#'
-#' * The `.data` pronoun is an object that represents the current
-#' slice of data. If you have a variable name in a string, use the
-#' `.data` pronoun to subset that variable with `[[`.
-#'
-#' ```
-#' my_var <- "disp"
-#' mtcars %>% summarise(mean = mean(.data[[my_var]]))
-#' ```
-#'
-#' * Another tidy eval operator is `:=`. It makes it possible to use
-#' glue and curly-curly syntax on the LHS of `=`. For technical
-#' reasons, the R language doesn't support complex expressions on
-#' the left of `=`, so we use `:=` as a workaround.
-#'
-#' ```
-#' my_function <- function(data, var, suffix = "foo") {
-#' # Use `{{` to tunnel function arguments and the usual glue
-#' # operator `{` to interpolate plain strings.
-#' data %>%
-#' summarise("{{ var }}_mean_{suffix}" := mean({{ var }}))
-#' }
-#' ```
-#'
-#' * Many tidy eval functions like `dplyr::mutate()` or
-#' `dplyr::summarise()` give an automatic name to unnamed inputs. If
-#' you need to create the same sort of automatic names by yourself,
-#' use `as_label()`. For instance, the glue-tunnelling syntax above
-#' can be reproduced manually with:
-#'
-#' ```
-#' my_function <- function(data, var, suffix = "foo") {
-#' var <- enquo(var)
-#' prefix <- as_label(var)
-#' data %>%
-#' summarise("{prefix}_mean_{suffix}" := mean(!!var))
-#' }
-#' ```
-#'
-#' Expressions defused with `enquo()` (or tunnelled with `{{`) need
-#' not be simple column names, they can be arbitrarily complex.
-#' `as_label()` handles those cases gracefully. If your code assumes
-#' a simple column name, use `as_name()` instead. This is safer
-#' because it throws an error if the input is not a name as expected.
-#'
-#' @md
-#' @name tidyeval
-#' @keywords internal
-#' @importFrom rlang enquo enquos .data := as_name as_label
-#' @aliases enquo enquos .data := as_name as_label
-#' @export enquo enquos .data := as_name as_label
-NULL
diff --git a/man/tidyeval.Rd b/man/tidyeval.Rd
deleted file mode 100644
index f773abf..0000000
--- a/man/tidyeval.Rd
+++ /dev/null
@@ -1,98 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils-tidy-eval.R
-\name{tidyeval}
-\alias{tidyeval}
-\alias{enquo}
-\alias{enquos}
-\alias{.data}
-\alias{:=}
-\alias{as_name}
-\alias{as_label}
-\title{Tidy eval helpers}
-\description{
-This page lists the tidy eval tools reexported in this package from
-rlang. To learn about using tidy eval in scripts and packages at a
-high level, see the \href{https://dplyr.tidyverse.org/articles/programming.html}{dplyr programming vignette}
-and the \href{https://ggplot2.tidyverse.org/articles/ggplot2-in-packages.html}{ggplot2 in packages vignette}.
-The \href{https://adv-r.hadley.nz/metaprogramming.html}{Metaprogramming section} of \href{https://adv-r.hadley.nz}{Advanced R} may also be useful for a deeper dive.
-\itemize{
-\item The tidy eval operators \verb{\{\{}, \verb{!!}, and \verb{!!!} are syntactic
-constructs which are specially interpreted by tidy eval functions.
-You will mostly need \verb{\{\{}, as \verb{!!} and \verb{!!!} are more advanced
-operators which you should not have to use in simple cases.
-
-The curly-curly operator \verb{\{\{} allows you to tunnel data-variables
-passed from function arguments inside other tidy eval functions.
-\verb{\{\{} is designed for individual arguments. To pass multiple
-arguments contained in dots, use \code{...} in the normal way.
-
-\if{html}{\out{}}\preformatted{my_function <- function(data, var, ...) \{
- data \%>\%
- group_by(...) \%>\%
- summarise(mean = mean(\{\{ var \}\}))
-\}
-}\if{html}{\out{
}}
-\item \code{\link[=enquo]{enquo()}} and \code{\link[=enquos]{enquos()}} delay the execution of one or several
-function arguments. The former returns a single expression, the
-latter returns a list of expressions. Once defused, expressions
-will no longer evaluate on their own. They must be injected back
-into an evaluation context with \verb{!!} (for a single expression) and
-\verb{!!!} (for a list of expressions).
-
-\if{html}{\out{}}\preformatted{my_function <- function(data, var, ...) \{
- # Defuse
- var <- enquo(var)
- dots <- enquos(...)
-
- # Inject
- data \%>\%
- group_by(!!!dots) \%>\%
- summarise(mean = mean(!!var))
-\}
-}\if{html}{\out{
}}
-
-In this simple case, the code is equivalent to the usage of \verb{\{\{}
-and \code{...} above. Defusing with \code{enquo()} or \code{enquos()} is only
-needed in more complex cases, for instance if you need to inspect
-or modify the expressions in some way.
-\item The \code{.data} pronoun is an object that represents the current
-slice of data. If you have a variable name in a string, use the
-\code{.data} pronoun to subset that variable with \code{[[}.
-
-\if{html}{\out{}}\preformatted{my_var <- "disp"
-mtcars \%>\% summarise(mean = mean(.data[[my_var]]))
-}\if{html}{\out{
}}
-\item Another tidy eval operator is \verb{:=}. It makes it possible to use
-glue and curly-curly syntax on the LHS of \code{=}. For technical
-reasons, the R language doesn't support complex expressions on
-the left of \code{=}, so we use \verb{:=} as a workaround.
-
-\if{html}{\out{}}\preformatted{my_function <- function(data, var, suffix = "foo") \{
- # Use `\{\{` to tunnel function arguments and the usual glue
- # operator `\{` to interpolate plain strings.
- data \%>\%
- summarise("\{\{ var \}\}_mean_\{suffix\}" := mean(\{\{ var \}\}))
-\}
-}\if{html}{\out{
}}
-\item Many tidy eval functions like \code{dplyr::mutate()} or
-\code{dplyr::summarise()} give an automatic name to unnamed inputs. If
-you need to create the same sort of automatic names by yourself,
-use \code{as_label()}. For instance, the glue-tunnelling syntax above
-can be reproduced manually with:
-
-\if{html}{\out{}}\preformatted{my_function <- function(data, var, suffix = "foo") \{
- var <- enquo(var)
- prefix <- as_label(var)
- data \%>\%
- summarise("\{prefix\}_mean_\{suffix\}" := mean(!!var))
-\}
-}\if{html}{\out{
}}
-
-Expressions defused with \code{enquo()} (or tunnelled with \verb{\{\{}) need
-not be simple column names, they can be arbitrarily complex.
-\code{as_label()} handles those cases gracefully. If your code assumes
-a simple column name, use \code{as_name()} instead. This is safer
-because it throws an error if the input is not a name as expected.
-}
-}
-\keyword{internal}