reduce example times and update vignette

UCLouvain-CBIO · Oct 13, 2023 · 85015d6 · 85015d6
1 parent 3ca56de
commit 85015d6
Show file tree

Hide file tree

Showing 13 changed files with 41 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CTexploreR
 Title: Explores Cancer Testis Genes
-Version: 0.99.3
+Version: 0.99.4
 Authors@R:
     c(person(given = "Axelle",
            family = "Loriot",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # CTexploreR 0.99
 
+## CTexploreR 0.99.4
+
+- Don't run some examples to save time. These functions are
+  illustrated in the vignette.
+
 ## CTexploreR 0.99.3
 
 - Reduce check time

diff --git a/R/CCLE_expression.R b/R/CCLE_expression.R
@@ -40,9 +40,11 @@
 #' @import CTdata
 #'
 #' @examples
+#' \dontrun{
 #' CCLE_expression(
 #'     genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "MAGEA10"),
 #'     type = c("Skin", "Lung"), units = "log_TPM")
+#' }
 CCLE_expression <- function(genes = NULL, type = NULL, units = "TPM",
                             return = FALSE) {
     suppressMessages({
@@ -82,7 +84,7 @@ CCLE_expression <- function(genes = NULL, type = NULL, units = "TPM",
         col = list(type = CCLE_colors))
 
     fontsize <- set_fontsize(mat)
-    
+
     if (length(type) <= 5) label_fontsize <- 6
     if (length(type) > 5 & length(type) < 10) label_fontsize <- 4
     if (length(type) >= 10 | is.null(type)) label_fontsize <- 0
@@ -107,4 +109,4 @@ CCLE_expression <- function(genes = NULL, type = NULL, units = "TPM",
         return(mat)
     }
     return(h)
-}
+}
diff --git a/R/CT_correlated_genes.R b/R/CT_correlated_genes.R
@@ -32,7 +32,9 @@
 #' @importFrom rlang .data
 #'
 #' @examples
+#' \dontrun{
 #' CT_correlated_genes(gene = "MAGEA3")
+#' }
 CT_correlated_genes <- function(gene, corr_thr = 0.5,
                                 return = FALSE) {
     suppressMessages({

diff --git a/R/TCGA_expression.R b/R/TCGA_expression.R
@@ -31,9 +31,11 @@
 #' @importFrom circlize colorRamp2
 #'
 #' @examples
+#' \dontrun{
 #' TCGA_expression(
 #'     tumor = "LUAD", genes = c("MAGEA1", "MAGEA3"),
 #'     units = "log_TPM")
+#' }
 TCGA_expression <- function(tumor = "all", genes = NULL,
                             units = "TPM", return = FALSE) {
     suppressMessages({

diff --git a/R/TCGA_methylation_expression_correlation.R b/R/TCGA_methylation_expression_correlation.R
@@ -50,7 +50,9 @@
 #' @importFrom rlang .data
 #'
 #' @examples
+#' \dontrun{
 #' TCGA_methylation_expression_correlation("LUAD", gene = "TDRD1")
+#' }
 TCGA_methylation_expression_correlation <- function(
     tumor = "all",
     gene = NULL,

diff --git a/R/testis_expression.R b/R/testis_expression.R
@@ -35,9 +35,10 @@
 #' @importFrom Biobase rowMax
 #'
 #' @examples
-#'
+#' \dontrun{
 #' testis_expression(cells = "germ_cells",
 #'                   genes = c("MAGEA1", "MAGEA3", "MAGEA4"))
+#' }
 testis_expression <- function(cells = "all", genes = NULL,
                               scale_lims = NULL, return = FALSE) {
     suppressMessages({

diff --git a/man/CCLE_expression.Rd b/man/CCLE_expression.Rd
diff --git a/man/CT_correlated_genes.Rd b/man/CT_correlated_genes.Rd
diff --git a/man/TCGA_expression.Rd b/man/TCGA_expression.Rd
diff --git a/man/TCGA_methylation_expression_correlation.Rd b/man/TCGA_methylation_expression_correlation.Rd
diff --git a/man/testis_expression.Rd b/man/testis_expression.Rd
diff --git a/vignettes/CTexploreR.Rmd b/vignettes/CTexploreR.Rmd
@@ -95,7 +95,7 @@ section). The table also summarises their main characteristics.
 
 ```{r CT_genes}
 library(CTexploreR)
-CT_genes
+head(CT_genes, 10)
 ```
 
 `CTdata` is the companion Package for `CTexploreR` and provides the omics
@@ -190,11 +190,13 @@ focused on true promoter regions.
 
 Genes flagged as `TRUE` in `regulated_by_methylation` column correspond to
 
-* Genes that are significantly induced by a demethylating agent (RNAseq analysis
-of cell lines reated with DAC (5-Aza-2′-Deoxycytidine)).
+* Genes that are significantly induced by a demethylating agent
+  (RNAseq analysis of cell lines reated with DAC
+  (5-Aza-2′-Deoxycytidine)).
 
-* Genes that have a highly methylated promoter in normal somatic tissues but
-less methylated in germ cells (WGBS analysis of a set of normal tissues).
+* Genes that have a highly methylated promoter in normal somatic
+  tissues but less methylated in germ cells (WGBS analysis of a set of
+  normal tissues).
 
 For some genes showing a strong activation in cells treated with
 5-Aza-2′-Deoxycytidine, methylation analysis was not possible due to
@@ -318,8 +320,9 @@ Allows to visualise gene expression in different histological types of CCLE
 cancer cell lines. We can thus compare genes that are or not activated in
 tumoral cell lines.
 
-* Applied to CT genes frequently activated in CCLE cell lines, more than 5% of
-CCLE cell_lines are expressing each gene. A string signal is visible.
+* Applied to CT genes frequently activated in CCLE cell lines, more
+  than 5% of CCLE cell_lines are expressing each gene. A string signal
+  is visible.
 
 ```{r}
 frequently_activated <- dplyr::filter(
@@ -339,9 +342,9 @@ CCLE_expression(
 
 
 
-* Applied to CT genes not frequently activated in CCLE cell lines, more than
-95% of cell lines are not expressing each genes. The lack of expression is very
-clear.
+* Applied to CT genes not frequently activated in CCLE cell lines,
+  more than 95% of cell lines are not expressing each genes. The lack
+  of expression is very clear.
 
 ```{r}
 not_frequently_activated <- dplyr::filter(