Hot fixes

.Rbuildignore

@@ -13,3 +13,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.lintr$

.lintr

@@ -0,0 +1,8 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"
+exclusions: list(
+    "vignettes/articles/filter.Rmd",
+    "vignettes/articles/filter2.Rmd",
+    "vignettes/articles/downstream_analyses.Rmd",
+    "vignettes/articles/reference_semantics.Rmd"
+  )

R/filter_pactr-methods.R

@@ -7,8 +7,8 @@ filter_pactr$set(
            max_iso_shift,
            merge_peaks,
            merge_method = NULL) {
-    cli::cli_alert_info("Checking {nrow(self$mpactr_data$get_peak_table())}
-                      peaks for mispicked peaks.")
+    l <- nrow(self$mpactr_data$get_peak_table())
+    cli::cli_alert_info("Checking {l} peaks for mispicked peaks.")
 
     ion_filter_list <- list()
     cut_ions <- c() # list
@@ -49,13 +49,14 @@ filter_pactr$set(
     self$logger[["check_mismatched_peaks"]] <- ion_filter_list
 
     if (isTRUE(merge_peaks)) {
-      cli::cli_alert_info("Argument merge_peaks is: {merge_peaks}.
-                         Merging mispicked peaks with method {merge_method}.")
+      cli::cli_alert_info(c("Argument merge_peaks is: {merge_peaks}. ",
+                            "Merging mispicked peaks with method ",
+                            "{merge_method}."))
 
       private$merge_ions(ion_filter_list, merge_method)
     } else {
-      cli::cli_alert_warning("Argument merge_peaks is: {merge_peaks}.
-                           Mispicked peaks will not be merged.")
+      cli::cli_alert_warning(c("Argument merge_peaks is: {merge_peaks}. ",
+                               "Mispicked peaks will not be merged."))
     }
 
     self$logger$list_of_summaries$mispicked <- summary$new(
@@ -111,8 +112,8 @@ filter_pactr$set("private", "get_merged_ions", function(ringwin,
 
 filter_pactr$set("private", "merge_ions", function(ion_filter_list, method) {
   if (is.null(method)) {
-    cli::cli_abort("No method has been supplied for merging peaks.
-                   method must be one of: sum")
+    cli::cli_abort(c("No method has been supplied for merging peaks. ",
+                     "{.var method} must be one of: sum"))
   }
 
   if (method == "sum") {
@@ -222,21 +223,23 @@ filter_pactr$set(
   function(group, remove_ions = TRUE) {
     groups <- unique(self$mpactr_data$get_meta_data()$Biological_Group)
     if (isFALSE(group %in% groups)) {
-      cli::cli_abort("{.var group} {group} is not in {.var Biological_Group}.
-                     Options are: {groups}")
+
+      cli::cli_abort(c("{.var group} {group} is not in ",
+                       "{.var Biological_Group}.",
+                       "Options are: {groups}"))
     }
 
-    cli::cli_alert_info("Parsing {nrow(self$mpactr_data$get_peak_table())}
-                      peaks based on the following sample group: {group}.")
+    l <- nrow(self$mpactr_data$get_peak_table())
+    cli::cli_alert_info("Parsing {l} peaks based on the sample group: {group}.")
 
     if (isFALSE(remove_ions)) {
-      cli::cli_alert_warning("Argument remove_ions is {remove_ions}.
-                           Peaks from {group} will not be removed.")
+      cli::cli_alert_warning(c("Argument remove_ions is {remove_ions}. ",
+                               "Peaks from {group} will not be removed."))
       return()
     }
 
-    cli::cli_alert_info("Argument remove_ions is: {remove_ions}.
-                      Removing peaks from {group}.")
+    cli::cli_alert_info(c("Argument remove_ions is: {remove_ions}.",
+                          "Removing peaks from {group}."))
 
     ions <- self$logger[["group_filter-failing_list"]][[group]]
     self$mpactr_data$set_peak_table(self$mpactr_data$get_peak_table()[
@@ -269,14 +272,15 @@ filter_pactr$set(
 
     ## abort if there are no technical replicates.
     if (isFALSE(self$mpactr_data$isMultipleTechReps())) {
-      cli::cli_abort("There are no technical replicates in the dataset
-                   provided. In order to run the replicability filter,
-                   technical replicates are required.")
+      cli_abort(c("There are no technical replicates in the dataset provided. ",
+                  "In order to run the replicability filter, technical ",
+                  "replicates are required."))
     }
 
     input_ions <- self$mpactr_data$get_peak_table()$Compound
-    cli::cli_alert_info("Parsing {length(input_ions)} peaks for
-                      replicability across technical replicates.")
+    cli <- cli::cli_alert_info
+    n <- length(input_ions)
+    cli("Parsing {n} peaks for replicability across technical replicates.")
 
     cv <- data.table::melt(self$mpactr_data$get_peak_table(),
       id.vars = c("Compound", "mz", "rt", "kmd"), variable.name =

R/filters.R

@@ -227,12 +227,14 @@ filter_group <- function(mpactr_object,
 #'
 #' data_filter <- filter_cv(data,
 #'   cv_threshold = 0.01,
-#'   cv_param = "mean"
+#'   cv_param = "mean",
+#'   copy_object = TRUE
 #' )
 #'
 #' data_filter <- filter_cv(data,
 #'   cv_threshold = 0.01,
-#'   cv_param = "median"
+#'   cv_param = "median",
+#'   copy_object = TRUE
 #' )
 #'
 filter_cv <- function(mpactr_object,
@@ -259,7 +261,6 @@ filter_cv <- function(mpactr_object,
   return(mpactr_object)
 }
 
-
 ###########################
 ### Insource ions filter ##
 ###########################

R/mpactr-methods.R

@@ -6,6 +6,7 @@ mpactr$set("private", "initialize_data", function() {
     private$peak_table[, .SD, .SDcols = private$meta_data$Injection]
   ) > 0), ]
   private$set_kmd()
+  private$peak_table$Compound <- as.character(private$peak_table$Compound)
 })
 mpactr$set("private", "set_kmd", function() {
   private$peak_table[, kmd := mz - floor(mz)]

R/peak_table_formatter.R

@@ -29,7 +29,6 @@ format_by_type <- function(peak_table_path,
   } # default condition = NULL
 }
 
-
 progenesis_formatter <- function(peak_table) {
   peak_table <- data.table(readr::read_csv(peak_table,
     skip = 2,
@@ -64,10 +63,6 @@ mz_mine_formatter <- function(peak_table) {
 metaboscape_formatter <- function(peak_table, sample_names) {
   peak_table <- data.table(readr::read_csv(peak_table, show_col_types = FALSE))
   peak_table_convert <- data.table::copy(peak_table)
-  adduct_data <- utils::read.csv(system.file("extdata/ion_masses",
-    "DefinedIons.csv",
-    package = "mpactR"
-  ))
   peak_table_convert <- with(peak_table_convert, peak_table_convert[
     , ion := gsub(
       ".*\\[(.+)\\].*", "\\1",
@@ -82,7 +77,10 @@ metaboscape_formatter <- function(peak_table, sample_names) {
   ][
     charge_string == "3+", charge := 3
   ][
-    adduct_data,
+    utils::read.csv(system.file("extdata/ion_masses",
+      "DefinedIons.csv",
+      package = "mpactR"
+    )),
     on = .(ion = IONS)
   ][
     , mz := (PEPMASS / charge) + MASS

R/summary-class.R

@@ -10,10 +10,12 @@ summary <- R6::R6Class("summary",
       private$passed_ions <- passed_ions
     },
     summarize = function(x) {
-      cli::cli_alert_success("{length(private$failed_ions)} ions failed the
-                              {private$filter} filter,
-                               {length(private$passed_ions)}
-                               ions remain.")
+      l <- length(private$failed_ions)
+      f <- private$filter
+      r <- length(private$passed_ions)
+
+      cli::cli_alert_success(c("{l} ions failed the {f} filter, ",
+                               "{r} ions remain."))
     },
     get_failed_ions = function() {
       return(private$failed_ions)