style: whitespace

Author: ethanbass

R/read_mzml.R

@@ -26,19 +26,20 @@
 
 read_mzml <- function(path, format_out = c("matrix", "data.frame"),
                       data_format = c("long","wide"),
-                      parser=c("RaMS","mzR"),
-                      what=c("MS1","MS2", "BPC", "TIC", "DAD",
+                      parser = c("RaMS","mzR"),
+                      what = c("MS1","MS2", "BPC", "TIC", "DAD",
                              "chroms", "metadata", "everything"),
                       verbose = FALSE,
                       ...){
   parser <- match.arg(parser, c("RaMS", "mzR"))
   format_out <- match.arg(format_out, c("matrix", "data.frame"))
   data_format <- match.arg(data_format, c("long","wide"))
   what <- match.arg(what, c("MS1","MS2", "BPC", "TIC", "DAD",
-                            "chroms", "metadata", "everything"), several.ok = TRUE)
+                            "chroms", "metadata", "everything"),
+                              several.ok = TRUE)
   if (all(c("MS1","MS2", "BPC", "TIC", "DAD",
             "chroms", "metadata", "everything") %in% what)){
-    what <- grep("everything",what, invert = TRUE,value = TRUE)
+    what <- grep("everything", what, invert = TRUE, value = TRUE)
   }
   if (parser == "RaMS"){
     data <- RaMS::grabMSdata(path, grab_what = what, verbosity = verbose, ...)

R/read_thermoraw.R

@@ -103,20 +103,23 @@ configure_thermo_parser <- function(reconfigure = FALSE, check = FALSE){
     exists <- file.exists(path_parser)
     if (!exists & !check){
       warning("ThermoRawFileParser not found!", immediate. = TRUE)
-      path_parser <- readline(prompt="Please provide path to `ThermoRawFileParser.exe`):")
+      path_parser <- readline(prompt = "Please provide path to `ThermoRawFileParser.exe`):")
       path_parser <- gsub("/", "\\\\", path_parser)
-      writeLines(path_parser, con=system.file('shell/path_parser.txt', package='chromConverter'))
+      writeLines(path_parser, con = system.file('shell/path_parser.txt',
+                                              package = 'chromConverter'))
     }
   } else {
-    shell_script <- readLines(system.file('shell/thermofileparser.sh', package='chromConverter'))
+    shell_script <- readLines(system.file('shell/thermofileparser.sh',
+                                          package = 'chromConverter'))
     path_parser <- strsplit(shell_script[2]," ")[[1]]
     path_parser <- path_parser[grep(".exe", path_parser)]
     exists <- file.exists(path_parser)
     if (!exists & !check){
       warning("ThermoRawFileParser not found!", immediate. = TRUE)
-      path_parser <- readline(prompt="Please provide path to `ThermoRawFileParser.exe`):")
+      path_parser <- readline(prompt = "Please provide path to `ThermoRawFileParser.exe`):")
       shell_script[2] <- paste0("mono ", path_parser, ' "$@"')
-      writeLines(shell_script, con = system.file('shell/thermofileparser.sh', package='chromConverter'))
+      writeLines(shell_script, con = system.file('shell/thermofileparser.sh',
+                                                 package = 'chromConverter'))
     }
   }
   if (check){