Major bug fixes and additions, fixing last commit

- renv:

	+ removed `renv` from dependencies
	+ deprecated `load_renv`
- added knitr to dependencies
- removed gene sampling for GO term enrichment which lead to different results for long gene lists
- fixed issue with exported function conflicting with other namespace
- added `prettycode`

DESCRIPTION

 Package: corescf
 Title: Collection of Useful CSF Functions
 Description: Collection of useful custom functions as part of the CSF workflows.
-Version: 0.8.2.7000
+Version: 0.8.2.9000
 Authors@R: c(
     person(given = "António",
            family = "Domingues",
@@ -22,7 +22,7 @@ Authors@R: c(
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
 biocViews:
 Depends:
@@ -50,7 +50,6 @@ Imports:
     RColorBrewer,
     docopt,
     session,
-    renv,
     ggdendro,
     grid,
     glue,

NAMESPACE

@@ -157,7 +157,6 @@ importFrom(plyr,splat)
 importFrom(purrr,discard)
 importFrom(purrr,map)
 importFrom(readr,read_tsv)
-importFrom(renv,load)
 importFrom(rlang,enexpr)
 importFrom(rlang,enquo)
 importFrom(rlang,get_expr)

R/cp_helpers.R

@@ -199,10 +199,6 @@ cp_test <- function(geneIds, annoDb, cp_species, q_cutoff = 0.05) {
   # DEBUG geneIds <- glMapped %>% ungroup %>% filter(contrast==contrast[1])$entrez_gene_id
   #    geneIds=.$entrez_gene_id
 
-  if (length(geneIds) > 1500) {
-    geneIds <- sample(geneIds) %>% head(1500)
-  }
-
   ## disable gene symbols output for yeast because it's not supported by underlying annotation db
   ## see also https://github.com/GuangchuangYu/clusterProfiler/issues/91
   readable <- cp_species != "yeast"

R/package_helpers.R

@@ -89,19 +89,11 @@ check_version <- function(pkg, min_version) {
 #'
 #' Loads a renv library if detect
 #'
-#' @importFrom renv load
 #'
 #' @return NULL
 #' @export
 load_renv <- function() {
-  scripts_dir <- Sys.getenv("PRJ_SCRIPTS")
-  lock_file <- file.path(scripts_dir, "renv.lock")
-  if (scripts_dir != "" & file.exists(lock_file)) {
-    message("Project variables were detected. Loading renv")
-    renv::load(project = Sys.getenv("PRJ_SCRIPTS"))
-  } else {
-    stop("renv not loaded: Bash variable PRJ_SCRIPTS was not found.")
-  }
+  .Defunct("load_renv")
 }
 
 
@@ -132,6 +124,7 @@ load_all <- function(verbose = FALSE) {
   load_pack("ggplot2")
   load_pack("scales", warn_conflicts = F) # note this has a known conflict with purrr::discard
   load_pack("grid")
+  load_pack("knitr")
   load_pack("RColorBrewer")
 
   ## for table exploration without using Rstudio
@@ -140,7 +133,7 @@ load_all <- function(verbose = FALSE) {
   ## replace masked functions with those of corescf
   assign("set_names", corescf::set_names, envir = .GlobalEnv)
   assign("frame_data", corescf::frame_data, envir = .GlobalEnv)
-
+  assign("distinct_all", corescf::distinct_all, envir = .GlobalEnv)
 }
 
 

R/system_helpers.R

@@ -24,7 +24,7 @@ cache_it <- function(expr, filePrefix = "cache") {
   if (file.exists(cacheFile)) {
     local(get(load(cacheFile)))
   } else {
-    result <- eval(expr)
+    result <- eval(expr, envir = .GlobalEnv)
     save(result, file = cacheFile)
     result
   }

man/ac.Rd

@@ -7,7 +7,7 @@
 ac(...)
 }
 \arguments{
-\item{...}{arguments to be passed to \code{\link[base:as.character]{base::as.character()}}}
+\item{...}{arguments to be passed to \code{\link[base:character]{base::as.character()}}}
 }
 \value{
 a string vector

man/add_rownames.Rd

@@ -7,7 +7,7 @@
 add_rownames(...)
 }
 \arguments{
-\item{...}{arguments to be passed to \code{\link[tibble:rownames_to_column]{tibble::rownames_to_column()}}}
+\item{...}{arguments to be passed to \code{\link[tibble:rownames]{tibble::rownames_to_column()}}}
 }
 \value{
 a tibble

man/as.df.Rd

@@ -13,5 +13,5 @@ as.df(dt)
 a data.frame
 }
 \description{
-DEPRECATED: use \code{\link[corescf:as_df]{corescf::as_df()}}
+DEPRECATED: use \code{\link[=as_df]{as_df()}}
 }

man/diff_intersect.Rd

@@ -13,7 +13,7 @@ diff_intersect(deData, sample_1, sample_twoes, .intersect_method, ...)
 
 \item{sample_twoes}{Conditions to intersect with}
 
-\item{.intersect_method}{Which function to use for the intersection? Example \code{\link[corescf:s1_gt_s2]{corescf::s1_gt_s2()}}}
+\item{.intersect_method}{Which function to use for the intersection? Example \code{\link[=s1_gt_s2]{s1_gt_s2()}}}
 
 \item{...}{Other methods passed to the intersection function}
 }

man/extract_col.Rd

@@ -11,15 +11,15 @@ extract_col(x, col_index = 1, sep = "_", num_cols = 10)
 
 \item{col_index}{Column index to retrieve, default is 1}
 
-\item{sep}{separator to split strings, default is "_". Argument of \code{\link[stringr:str_split_fixed]{stringr::str_split_fixed()}}}
+\item{sep}{separator to split strings, default is "_". Argument of \code{\link[stringr:str_split]{stringr::str_split_fixed()}}}
 
-\item{num_cols}{maximum number of columns returned by \code{\link[stringr:str_split_fixed]{stringr::str_split_fixed()}}, default is 10. Argument of \code{\link[stringr:str_split_fixed]{stringr::str_split_fixed()}}}
+\item{num_cols}{maximum number of columns returned by \code{\link[stringr:str_split]{stringr::str_split_fixed()}}, default is 10. Argument of \code{\link[stringr:str_split]{stringr::str_split_fixed()}}}
 }
 \value{
 character vector
 }
 \description{
-convenience method to extract a column, defaults to _ as separator and the first column. A wrapper around \link[stringr:str_split_fixed]{stringr::str_split_fixed}. I will take a string vector, separate the elements according to a pattern, and return a particular column from the resulting matrix
+convenience method to extract a column, defaults to _ as separator and the first column. A wrapper around \link[stringr:str_split]{stringr::str_split_fixed}. I will take a string vector, separate the elements according to a pattern, and return a particular column from the resulting matrix
 }
 \examples{
 \dontrun{

man/filter_expressed_genes.Rd

@@ -11,7 +11,7 @@ filter_expressed_genes(df, id_col = "ensembl_gene_id", ...)
 
 \item{id_col}{the column with gene identifiers. Default ensembl_gene_id}
 
-\item{...}{Arguments to be passed to \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}}
+\item{...}{Arguments to be passed to \code{\link[=filterByExpression]{filterByExpression()}}}
 }
 \value{
 A data.frame

man/getExpressedGenes.Rd

@@ -15,7 +15,7 @@ getExpressedGenes(cuff, ...)
 A matrix
 }
 \description{
-Wrapper for \code{\link[cummeRbund:repFpkmMatrix]{cummeRbund::repFpkmMatrix()}} and \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}
+Wrapper for \code{\link[cummeRbund:fpkmMatrix]{cummeRbund::repFpkmMatrix()}} and \code{\link[=filterByExpression]{filterByExpression()}}
 }
 \note{
 cummeRbund is now very old and has been superseded by better tools. It should not be the first choice for gene expression analysis.

man/lsosh.Rd

@@ -23,7 +23,7 @@ lsosh(..., n = 10)
 data.frame
 }
 \description{
-Wrapper of \code{\link[corescf:lsos]{corescf::lsos()}} to just shows top 10 results
+Wrapper of \code{\link[=lsos]{lsos()}} to just shows top 10 results
 }
 \examples{
 \dontrun{

man/pretty_columns.Rd

@@ -14,5 +14,5 @@ a data.frame
 }
 \description{
 Removes funky characters from colnames, and converts to lower case, to make them suitable for computational work
-Uses \code{\link[corescf:pretty_names]{corescf::pretty_names()}}
+Uses \code{\link[=pretty_names]{pretty_names()}}
 }

man/retainExprGenes.Rd

@@ -11,8 +11,8 @@ retainExprGenes(df, id_col = "ensembl_gene_id", ...)
 
 \item{id_col}{the column with gene identifiers. Default ensembl_gene_id}
 
-\item{...}{Arguments to be passed to \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}}
+\item{...}{Arguments to be passed to \code{\link[=filterByExpression]{filterByExpression()}}}
 }
 \description{
-#' Deprecated, use \code{\link[corescf:filter_expressed_genes]{corescf::filter_expressed_genes()}} instead.
+#' Deprecated, use \code{\link[=filter_expressed_genes]{filter_expressed_genes()}} instead.
 }

man/rownames2column.Rd

@@ -15,7 +15,7 @@ rownames2column(df, colname)
 a data.frame
 }
 \description{
-Deprecated, use \code{\link[tibble:rownames_to_column]{tibble::rownames_to_column()}} instead.
+Deprecated, use \code{\link[tibble:rownames]{tibble::rownames_to_column()}} instead.
 }
 \details{
 tibbles usually don't have row names, nor are they kept in the conversion, so this function is needed to keep them as an extra column.

man/select.Rd

@@ -11,5 +11,5 @@ a function
 }
 \description{
 Select is a very common verb which appears in at least 3 packages. This function makes sure it's defaults to dplyr which is the most commonly used
-Call \code{\link[MASS:select]{MASS::select()}}, \code{\link[tidygraph:select]{tidygraph::select()}}, or  \code{\link[AnnotationDbi:select]{AnnotationDbi::select()}} for other usages
+Call \code{\link[MASS:lm.ridge]{MASS::select()}}, \code{\link[tidygraph:reexports]{tidygraph::select()}}, or  \code{\link[AnnotationDbi:AnnotationDb-class]{AnnotationDbi::select()}} for other usages
 }

man/vec2df.Rd

@@ -13,7 +13,7 @@ vec2df(namedVec)
 a data.frame
 }
 \description{
-Deprecated, use \code{\link[corescf:vec_as_df]{corescf::vec_as_df()}} instead.
+Deprecated, use \code{\link[=vec_as_df]{vec_as_df()}} instead.
 }
 \examples{
 \dontrun{