fix: replace ceilingnumber by pretty to format Y scale, closes #18

Author: m-jahn

R/geom_coverage.R

@@ -26,14 +26,15 @@
 #' @return Layers of ggplot2.
 #' @importFrom ggplot2 aes_string scale_fill_manual geom_rect geom_text aes geom_step
 #' @importFrom rlang .data
-#' @importFrom grDevices colorRampPalette
+#' @importFrom grDevices colorRampPalette col2rgb
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom rlang as_label
 #' @importFrom stats as.formula
 #' @importFrom ggh4x facet_wrap2 strip_themed elem_list_rect
 #' @importFrom dplyr group_by summarise
 #' @importFrom magrittr %>%
 #' @importFrom ggrepel geom_text_repel
+#' @importFrom utils tail
 #'
 #' @export
 #' @examples
@@ -259,8 +260,8 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
       data.range <- data %>%
         dplyr::group_by(.data[[facet.key]]) %>%
         dplyr::summarise(.groups = "drop_last",
-                         min_score = CeilingNumber(min(.data[[ymax.str]])),
-                         max_score = CeilingNumber(max(.data[[ymax.str]]))
+                         min_score = pretty(.data[[ymax.str]])[1],
+                         max_score = tail(pretty(.data[[ymax.str]]), 1)
         )
       data.range$label <- paste0("[", data.range$min_score, ", ", data.range$max_score, "]")
       region.range <- geom_text(

R/geom_protein.R

@@ -35,13 +35,13 @@
 #' @export
 #'
 #' @examples
-#' # library(ggplot2)
-#' # library(ggcoverage)
-#' # coverage.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.xlsx", package = "ggcoverage")
-#' # fasta.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.fasta", package = "ggcoverage")
-#' # protein.id = "sp|
-#' # ggplot() +
-#' #     geom_peptide(coverage.file = coverage.file, fasta.file = fasta.file, protein.id = protein.id)
+#' library(ggplot2)
+#' library(ggcoverage)
+#' coverage.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.xlsx", package = "ggcoverage")
+#' fasta.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.fasta", package = "ggcoverage")
+#' protein.id = "sp|P02769|ALBU_BOVIN"
+#' ggplot() +
+#'   geom_protein(coverage.file = coverage.file, fasta.file = fasta.file, protein.id = protein.id)
 geom_protein <- function(coverage.file, fasta.file, protein.id, XCorr.threshold = 2,
                          confidence = "High", contaminant = NULL, remove.na = TRUE,
                          color = "grey", mark.bare = TRUE, mark.color = "red", mark.alpha = 0.5,
@@ -187,7 +187,7 @@ geom_protein <- function(coverage.file, fasta.file, protein.id, XCorr.threshold
   # range position
   if (range.position == "in") {
     # prepare range
-    max.abundance <- CeilingNumber(max(coverage.final$abundance))
+    max.abundance <- max(pretty(coverage.final$abundance))
     abundance.range <- data.frame(label = paste0("[0, ", scales::scientific(max.abundance, digits = 2), "]"))
     range.text <- geom_text(
       data = abundance.range,

R/theme_ggcoverage.R

@@ -20,7 +20,10 @@ theme_coverage <- function(space = 0.2) {
       axis.title = element_blank()
     ),
     ggplot2::annotate("segment", x = -Inf, xend = Inf, y = -Inf, yend = -Inf, size = rel(1)),
-    scale_y_continuous(expand = expansion(mult = c(0))),
+    scale_y_continuous(
+      limits = ~ c(pretty(.x)[1], tail(pretty(.x), 1)),
+      expand = expansion(mult = c(0))
+    ),
     scale_x_continuous(labels = scales::comma, expand = c(0, 0))
   )
 }
@@ -39,7 +42,7 @@ theme_coverage <- function(space = 0.2) {
 theme_coverage2 <- function(space = 0.2) {
   list(
     scale_y_continuous(
-      limits = ~ c(0, CeilingNumber(max(.x))),
+      limits = ~ range(pretty(.x)),
       breaks = ~ .x[2],
       expand = expansion(mult = c(0))
     ),
@@ -484,7 +487,7 @@ theme_cnv <- function(x.range, margin.len) {
   )
 }
 
-# theme for ggprotein: suitable for range position is in
+# theme for ggprotein: suitable for range.position = "in"
 #' Theme for geom_protein.
 #'
 #' @return List of layers.
@@ -508,7 +511,7 @@ theme_protein <- function() {
   )
 }
 
-# theme for ggprotein: suitable for range position is out
+# theme for ggprotein: suitable for range.position = "out"
 #' Theme for geom_protein.
 #'
 #' @return List of layers.
@@ -520,7 +523,7 @@ theme_protein <- function() {
 theme_protein2 <- function() {
   list(
     scale_y_continuous(
-      limits = ~ c(0, CeilingNumber(max(.x)), digits = 2),
+      limits = ~ range(pretty(.x)),
       breaks = ~ .x[2],
       expand = expansion(mult = c(0)),
       labels = function(x) format(x, scientific = TRUE, digits = 2)

R/utils.R

@@ -64,25 +64,6 @@ AutoColor <- function(data, n, name, key) {
   return(fill.color)
 }
 
-# ceiling for number bigger than zero, floor for number smaller than zero
-CeilingNumber <- function(x, digits = 2) {
-  if (x == 0) {
-    "0"
-  } else if (abs(x) >= 10^6) {
-    formatC(x, format = "e", digits = 2)
-  } else if (abs(x) >= 10000) {
-    formatC(round(x), format = "f", digits = 0)
-  } else if (abs(x) >= 1) {
-    if ((x %% floor(x)) != 0) {
-      formatC(x, format = "f", digits = 2)
-    } else {
-      formatC(x, format = "f", digits = 0)
-    }
-  } else {
-    formatC(x, format = "f", digits = 2)
-  }
-}
-
 # create aa plot dataframe with padding offset
 AAPadding <- function(len, offset = 0, aa.seq) {
   aa.seq.full <- rep(aa.seq, each = 3)