fixes for BiocCheck

line length and indents

Author: grlloyd

DESCRIPTION

@@ -21,8 +21,8 @@ Description: A package to merge, filter sort, organise and otherwise mash
     imported from multiple sources (software) and combined using workflow 
     steps based on S4
     class templates derived from the `struct` package. Other modular workflow
-    such as filtering, merging, splitting, normalisation and rest-api queries
-    are also included.
+    steps such as filtering, merging, splitting, normalisation and rest-api 
+    queries are included.
 License: GPL-3
 Encoding: UTF-8
 LazyData: false
@@ -38,10 +38,10 @@ Imports:
     httr,
     scales,
     ggthemes,
-    cowplot,
     ggplot2,
     utils,
-    rlang
+    rlang,
+    cowplot
 Collate: 
     'generics.R'
     'zzz.R'
@@ -114,6 +114,7 @@ Collate:
     'rdata_database_class.R'
     'rds_database_class.R'
     'rds_cache_class.R'
+    'remove_columns_class.R'
     'rename_columns_class.R'
     'rt_match_class.R'
     'select_columns_class.R'

NAMESPACE

@@ -80,6 +80,7 @@ export(pubchem_widget)
 export(rdata_database)
 export(rds_cache)
 export(rds_database)
+export(remove_columns)
 export(rename_columns)
 export(rest_api)
 export(rt_match)
@@ -106,7 +107,6 @@ import(ggplot2)
 import(ggthemes)
 import(httr)
 import(methods)
-import(patchwork)
 import(rlang)
 import(struct)
 importFrom(scales,manual_pal)

R/AnnotationDb_select_class.R

@@ -123,45 +123,45 @@ setMethod(
     definition = function(M, D) {
         # get db
         db <- do.call(`::`, list(M$database, M$database))
-        
+
         # prepare from:to for left join
         by <- M$key_type
         names(by) <- M$key_column
-        
+
         # columns
         if (any(M$database_columns == ".all")) {
             M$database_columns <- AnnotationDbi::columns(db)
         }
-        
+
         # select
-        db = AnnotationDbi::select(
+        db <- AnnotationDbi::select(
             x = db,
             keys = as.character(D$data[[M$key_column]]),
             columns = M$database_columns,
             keytype = M$key_type
         )
-        
+
         # remove NA
         if (M$drop_na) {
             na <- apply(db, 1, function(x) {
                 any(is.na(x))
             })
             db <- db[!na, ]
         }
-        
+
         # unique rows
         db <- unique(db)
-        
+
         # add the columns
         M2 <- add_columns(
             new_columns = db,
             by = by
         )
         M2 <- model_apply(M2, D)
-        
+
         # assign to object
         M$updated <- predicted(M2)
-        
+
         return(M)
     }
 )

R/BiocFileCache_database_class.R

@@ -159,15 +159,15 @@ setMethod(
         field = "rtype", query = "web"
     )$rid) {
         # TRUE if newly added or stale
-        update = BiocFileCache::bfcneedsupdate(bfc, rid)
+        update <- BiocFileCache::bfcneedsupdate(bfc, rid)
         if (is.na(update)) { # FALSE if NA
-            update=FALSE
+            update <- FALSE
         }
     } else {
-        update = FALSE # cant update if not web resource
+        update <- FALSE # cant update if not web resource
     }
-    
-    
+
+
     # download & unzip
     if (update & !obj$offline) {
         BiocFileCache::bfcdownload(

R/MTox700plus_database_class.R

@@ -57,7 +57,8 @@ MTox700plus_database <- function(version = "latest",
             description = paste0(
                 "The version number of the MTox700+ database to import. ",
                 "Available versions are listed here: ",
-                "[https://github.com/michabohealthscience/MTox700plus/releases].",
+                '[https://github.com/michabohealthscience/MTox700plus/',
+                'releases].',
                 ' `version` should match the tag of the release e.g. `"v1.0"`.',
                 ' For convenience `version = "latest"` will always retrieve ',
                 "the most recent release. To prevent unecessary downloads ",

R/MetMashR-package.R

@@ -1,5 +1,4 @@
 #' @import struct
-#' @import patchwork
 #' @importFrom utils URLencode modifyList read.csv stack unzip
 #' @keywords internal
 "_PACKAGE"

R/annotation_bar_chart.R

@@ -1,13 +1,12 @@
 #' @eval get_description('annotation_pie_chart')
 #' @include annotation_source_class.R
 #' @export
-annotation_bar_chart <- function(
-        factor_name,
-        label_rotation = FALSE,
-        label_location = "inside",
-        label_type = "percent",
-        legend = FALSE,
-        ...) {
+annotation_bar_chart <- function(factor_name,
+                                 label_rotation = FALSE,
+                                 label_location = "inside",
+                                 label_type = "percent",
+                                 legend = FALSE,
+                                 ...) {
     out <- struct::new_struct(
         "annotation_bar_chart",
         factor_name = factor_name,
@@ -17,7 +16,7 @@ annotation_bar_chart <- function(
         legend = legend,
         ...
     )
-    
+
     return(out)
 }
 
@@ -111,8 +110,8 @@ setMethod(
         df <- dobj$data %>%
             group_by(.data[[obj$factor_name]]) %>%
             summarise(count = n()) %>%
-            tidyr::complete(.data[[obj$factor_name]],fill=list(count=0))
-        
+            tidyr::complete(.data[[obj$factor_name]], fill = list(count = 0))
+
         # labels
         df$label <- ""
         if (obj$label_type == "percent") {
@@ -122,7 +121,7 @@ setMethod(
         } else if (obj$label_type == "count") {
             df$label <- as.character(df$count)
         }
-        
+
         if (obj$label_rotation) {
             df$label <- paste0(" ", df$label, " ")
         } else {
@@ -132,7 +131,7 @@ setMethod(
                 df$label <- paste0(df$label)
             }
         }
-        
+
         # add newlines of spaces to offset depending on rotation
         if (!obj$legend) {
             if (obj$label_type != "none") {
@@ -144,13 +143,13 @@ setMethod(
                 df$label <- df[[obj$factor_name]]
             }
         }
-        
+
         if (!obj$label_rotation) {
             df$rotate <- 0
         } else {
             df$rotate <- -90
         }
-        
+
         df$hjust <- 0.5
         if (obj$label_rotation) {
             if (obj$label_location == "inside") {
@@ -159,7 +158,7 @@ setMethod(
                 df$hjust <- 1
             }
         }
-        
+
         # plot
         g <- ggplot(
             data = df,
@@ -183,15 +182,15 @@ setMethod(
             structToolbox:::theme_Publication(12) +
             scale_fill_Publication() +
             theme_Publication()
-        
+
         # legend
         if (!obj$legend) {
             g <- g + theme(legend.position = "none")
         } else {
             g <- g + theme(axis.text.x = element_blank())
         }
-        
-        
+
+
         return(g)
     }
 )

R/annotation_pie_chart.R

@@ -1,21 +1,20 @@
 #' @eval get_description('annotation_pie_chart')
 #' @export
-annotation_pie_chart <- function(
-        factor_name,
-        label_rotation = FALSE,
-        label_location = "inside",
-        label_type = "percent",
-        legend = FALSE,
-        pie_rotation = 0,
-        centre_radius = 0,
-        centre_label = NULL,
-        count_na = FALSE,
-        ...) {
+annotation_pie_chart <- function(factor_name,
+                                 label_rotation = FALSE,
+                                 label_location = "inside",
+                                 label_type = "percent",
+                                 legend = FALSE,
+                                 pie_rotation = 0,
+                                 centre_radius = 0,
+                                 centre_label = NULL,
+                                 count_na = FALSE,
+                                 ...) {
     check <- centre_radius >= 0 & centre_radius <= 1
     if (!check) {
         stop("Pie chart centre_radius must be between 0 and 1.")
     }
-    
+
     out <- struct::new_struct(
         "annotation_pie_chart",
         factor_name = factor_name,
@@ -29,7 +28,7 @@ annotation_pie_chart <- function(
         count_na = count_na,
         ...
     )
-    
+
     return(out)
 }
 
@@ -47,7 +46,7 @@ annotation_pie_chart <- function(
         centre_radius = "entity",
         centre_label = "entity",
         count_na = "entity",
-        .pie_data = 'data.frame'
+        .pie_data = "data.frame"
     ),
     prototype = list(
         name = "Annotation pie chart",
@@ -165,13 +164,13 @@ setMethod(
     definition = function(obj, dobj) {
         r1 <- obj$centre_radius
         radians <- obj$pie_rotation * pi / 180
-        
+
         if (obj$label_location == "inside") {
             offset <- 1
         } else {
             offset <- 1.6
         }
-        
+
         if (obj$count_na) {
             dobj$data[[obj$factor_name]] <-
                 factor(dobj$data[[obj$factor_name]])
@@ -180,8 +179,8 @@ setMethod(
         df <- dobj$data %>%
             group_by(.data[[obj$factor_name]]) %>%
             summarise(count = n()) %>%
-            tidyr::complete(.data[[obj$factor_name]],fill=list(count=0))
-        
+            tidyr::complete(.data[[obj$factor_name]], fill = list(count = 0))
+
         # labels
         df$label <- ""
         if (obj$label_type == "percent") {
@@ -191,7 +190,7 @@ setMethod(
         } else if (obj$label_type == "count") {
             df$label <- as.character(df$count)
         }
-        
+
         if (!obj$legend) {
             if (obj$label_type != "none") {
                 df$label <- paste0(
@@ -202,7 +201,7 @@ setMethod(
                 df$label <- df[[obj$factor_name]]
             }
         }
-        
+
         # position of label in degrees
         df$angle <- ((cumsum(df$count) - (df$count / 2)) / sum(df$count)) *
             360 - obj$pie_rotation
@@ -211,13 +210,13 @@ setMethod(
         # centre if at top or bottom
         df$hjust[df$angle > 175 & df$angle < 185] <- 0.5
         df$hjust[df$angle > 355 | df$angle < 5] <- 0.5
-        
+
         if (!obj$label_rotation) {
             df$rotate <- 0
         } else {
             df$rotate <- df$angle - 270 - (180 * df$hjust)
         }
-        
+
         # plot
         g <- ggplot(
             data = df,
@@ -233,18 +232,18 @@ setMethod(
             coord_polar("y", start = radians, clip = "off") +
             theme_void() +
             geom_text(aes(x = offset, label = .data[["label"]], angle = rotate),
-                      position = position_stack(vjust = 0.5),
-                      hjust = df$hjust,
+                position = position_stack(vjust = 0.5),
+                hjust = df$hjust,
             ) +
             theme(plot.margin = unit(c(1, 1, 1, 1), "lines")) +
             xlim(c(0.5, 1.6)) +
             scale_fill_Publication()
-        
+
         # legend
         if (!obj$legend) {
             g <- g + theme(legend.position = "none")
         }
-        
+
         # add centre label
         if (!is.null(obj$centre_label)) {
             if (obj$centre_label == ".total") {
@@ -255,8 +254,8 @@ setMethod(
             g <- g +
                 geom_text(aes(x = 0.5, y = 0), label = obj$centre_label)
         }
-        
-        obj@.pie_data = df
+
+        obj@.pie_data <- df
         return(g)
     }
 )