Fix a couple of long lines

Author: csoneson

R/digestFastqs.R

@@ -382,7 +382,7 @@ digestFastqs <- function(fastqForward, fastqReverse = NULL,
                          maxNReads = -1, verbose = FALSE,
                          nThreads = 1, chunkSize = 100000,
                          maxReadLength = 1024) {
-    ## pre-flight checks ---------------------------------------------------------
+    ## pre-flight checks ------------------------------------------------------
     ## deprecated arguments
     deprecMessageColl <- paste0(
         "Starting from mutscan v0.3.0, collapsing of variable sequences is ", 
@@ -704,7 +704,8 @@ digestFastqs <- function(fastqForward, fastqReverse = NULL,
         !all(grepl("^[ACGTMRWSYKVHDBN]{3}$", 
                    toupper(forbiddenMutatedCodonsReverse)) |
              forbiddenMutatedCodonsReverse == "")) {
-        stop("All elements of 'forbiddenMutatedCodonsForward' and 'forbiddenMutatedCodonsReverse' must be ",
+        stop("All elements of 'forbiddenMutatedCodonsForward' and ", 
+             "'forbiddenMutatedCodonsReverse' must be ",
              "character strings consisting of three valid IUPAC letters.")
     } else {
         forbiddenMutatedCodonsForward <- toupper(forbiddenMutatedCodonsForward)
@@ -754,8 +755,10 @@ digestFastqs <- function(fastqForward, fastqReverse = NULL,
         normalizePath(filteredReadsFastqReverse, mustWork = FALSE)
 
     if ((any(fastqReverse == "") && filteredReadsFastqReverse != "") ||
-        (all(fastqReverse != "") && filteredReadsFastqForward != "" && filteredReadsFastqReverse == "") ||
-        (all(fastqForward != "") && filteredReadsFastqForward == "" && filteredReadsFastqReverse != "")) {
+        (all(fastqReverse != "") && filteredReadsFastqForward != "" && 
+         filteredReadsFastqReverse == "") ||
+        (all(fastqForward != "") && filteredReadsFastqForward == "" && 
+         filteredReadsFastqReverse != "")) {
         stop("The pairing of the output FASTQ files must be compatible ", 
              "with that of the input files.")
     }

R/plotPairs.R

@@ -147,9 +147,9 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
             )
     }
 
-    ## ----------------------------------------------------------------------- ##
+    ## --------------------------------------------------------------------- ##
     ## Scatter plots
-    ## ----------------------------------------------------------------------- ##
+    ## --------------------------------------------------------------------- ##
     if (pointsType == "smoothscatter") {
         ## Define function to create smoothscatter-like plot 
         ## (for use with ggpairs)

vignettes/mutscan.Rmd

@@ -611,7 +611,8 @@ that for this, at least two replicates are required.
 We start by looking at the design matrix, in order to determine which of the 
 coefficients to specify for the testing in `calculateRelativeFC()`. For more 
 information about how to set up and interpret design matrices in `edgeR` or 
-`limma`, see e.g. [Law et al (2020)](https://f1000research.com/articles/9-1444), 
+`limma`, see e.g. 
+[Law et al (2020)](https://f1000research.com/articles/9-1444), 
 or [Soneson et al (2020)](https://f1000research.com/articles/9-512).
 
 ```{r def-mm}