fix: remove conflicting package ggpp from geom_protein; closes #21

Author: m-jahn

DESCRIPTION

@@ -56,7 +56,7 @@ Imports:
     BiocParallel,
     openxlsx,
     stringr,
-    ggpp
+    gridExtra
 Suggests: 
     rmarkdown,
     knitr,

NAMESPACE

@@ -122,10 +122,11 @@ importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,unit)
-importFrom(ggpp,annotate)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
+importFrom(gridExtra,tableGrob)
+importFrom(gridExtra,ttheme_default)
 importFrom(magrittr,"%>%")
 importFrom(methods,extends)
 importFrom(openxlsx,read.xlsx)

R/geom_protein.R

@@ -14,7 +14,7 @@
 #' @param show.table Logical value, whether to show coverage summary table. Default: TRUE.
 #' @param table.position The position of the coverage summary table, choose from right_top, left_top, left_bottom, right_bottom.
 #' Default: right_top.
-#' @param table.size The font size of coverage summary table. Default: 4.
+#' @param table.size The font size of coverage summary table. Default: 12.
 #' @param table.color The font color of coverage summary table. Default: black.
 #' @param range.size The label size of range text, used when \code{range.position} is in. Default: 3.
 #' @param range.position The position of y axis range, chosen from in (move y axis in the plot) and
@@ -30,8 +30,8 @@
 #' @importFrom GenomicRanges reduce GRanges setdiff
 #' @importFrom IRanges IRanges
 #' @importFrom ggplot2 ggplot geom_rect geom_text aes aes_string
-#' @importFrom ggpp annotate
 #' @importFrom scales scientific
+#' @importFrom gridExtra ttheme_default tableGrob
 #' @export
 #'
 #' @examples
@@ -49,7 +49,7 @@
 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,
-                         show.table = TRUE, table.position = c("right_top", "left_top", "left_bottom", "right_bottom"),
+                         show.table = TRUE, table.position = c("top_right", "top_left", "bottom_right", "bottom_left"),
                          table.size = 4, table.color = "black", range.size = 3, range.position = c("in", "out")) {
   # check parameters
   table.position <- match.arg(arg = table.position)
@@ -169,22 +169,37 @@ geom_protein <- function(coverage.file, fasta.file, protein.id, XCorr.threshold
   # summary table
   if (show.table) {
     # table position
-    if (table.position == "left_top") {
-      table.x <- 0
-      table.y <- max(coverage.final[, "abundance"])
-    } else if (table.position == "right_top") {
-      table.x <- nchar(aa.seq.used)
-      table.y <- max(coverage.final[, "abundance"])
-    } else if (table.position == "left_bottom") {
-      table.x <- 0
-      table.y <- 0
-    } else if (table.position == "right_bottom") {
-      table.x <- nchar(aa.seq.used)
-      table.y <- 0
+
+    if (table.position == "top_left") {
+      table_xmin <- 0
+      table_xmax <- nchar(aa.seq.used) * 0.5
+      table_ymin <- max(coverage.final[, "abundance"]) * 0.5
+      table_ymax <- max(coverage.final[, "abundance"]) * 1.0
+    } else if (table.position == "top_right") {
+      table_xmin <- nchar(aa.seq.used) * 0.5
+      table_xmax <- nchar(aa.seq.used) * 1.0
+      table_ymin <- max(coverage.final[, "abundance"]) * 0.5
+      table_ymax <- max(coverage.final[, "abundance"]) * 1.0
+    } else if (table.position == "bottom_left") {
+      table_xmin <- 0
+      table_xmax <- nchar(aa.seq.used) * 0.5
+      table_ymin <- 0
+      table_ymax <- max(coverage.final[, "abundance"]) * 0.5
+    } else if (table.position == "bottom_right") {
+      table_xmin <- nchar(aa.seq.used) * 0.5
+      table_xmax <- nchar(aa.seq.used) * 1.0
+      table_ymin <- 0
+      table_ymax <- max(coverage.final[, "abundance"]) * 0.5
     }
-    summary.table <- ggpp::annotate(
-      geom = "table", label = list(coverage.summary), x = table.x, y = table.y,
-      color = table.color, size = table.size
+    table_theme <- gridExtra::ttheme_default(
+      base_size = table.size, base_colour = table.color
+    )
+    summary.table <- ggplot2::annotation_custom(
+      grob = gridExtra::tableGrob(
+        d = coverage.summary,
+        theme = table_theme),
+      xmin = table_xmin, xmax = table_xmax,
+      ymin = table_ymin, ymax = table_ymax
     )
     plot.ele <- append(plot.ele, summary.table)
   }

R/ggprotein.R

@@ -21,40 +21,28 @@
 #' out (normal y axis). Default: in.
 #'
 #' @return A ggplot2 object.
-#' @importFrom openxlsx read.xlsx
-#' @importFrom magrittr %>%
-#' @importFrom dplyr filter group_by summarise arrange
-#' @importFrom rlang .data
-#' @importFrom Biostrings readAAStringSet
-#' @importFrom stringr str_locate
-#' @importFrom GenomicRanges reduce GRanges setdiff
-#' @importFrom IRanges IRanges
-#' @importFrom ggplot2 ggplot geom_rect geom_text aes aes_string scale_x_continuous theme_classic theme
-#' element_blank annotate rel scale_y_continuous expansion
-#' @importFrom ggpp annotate
-#' @importFrom scales scientific
 #' @export
 #'
 #' @examples
-#' # 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"
-#' #
-#' # ggprotein(
-#' #   coverage.file = coverage.file,
-#' #   fasta.file = fasta.file,
-#' #   protein.id = protein.id
-#' # )
+#' 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"
+#'
+#' ggprotein(
+#'   coverage.file = coverage.file,
+#'   fasta.file = fasta.file,
+#'   protein.id = protein.id
+#' )
 ggprotein <- 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,
-                      show.table = TRUE, table.position = c("right_top", "left_top", "left_bottom", "right_bottom"),
-                      table.size = 4, table.color = "black", range.size = 3, range.position = c("in", "out")) {
+                      show.table = TRUE, table.position = c("top_right", "top_left", "bottom_left", "bottom_right"),
+                      table.size = 10, table.color = "black", range.size = 3, range.position = c("in", "out")) {
   # check parameters
   table.position <- match.arg(arg = table.position)
   range.position <- match.arg(arg = range.position)

README.Rmd

@@ -779,7 +779,7 @@ protein_set
 
 ### Protein coverage
 
-```{r basic_coverage_protein, warning=FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein, warning=FALSE, fig.height = 6, fig.width = 10, fig.align = "center"}
 protein_coverage <- ggprotein(
   coverage.file = coverage_file,
   fasta.file = fasta_file,
@@ -794,7 +794,7 @@ protein_coverage
 
 We can obtain features of the protein from [UniProt](https://www.uniprot.org/). For example, the above protein coverage plot shows that there is empty region in 1-24, and this empty region in [UniProt](https://www.uniprot.org/uniprotkb/P02769/entry) is annotated as Signal peptide and Propeptide peptide. When the protein is mature and released extracellular, these peptides will be cleaved. This is the reason why there is empty region in 1-24.
 
-```{r basic_coverage_protein_feature, warning=FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein_feature, warning=FALSE, fig.height = 6, fig.width = 10, fig.align = "center"}
 # protein feature obtained from UniProt
 protein_feature_df <- data.frame(
   ProteinID = "sp|P02769|ALBU_BOVIN",

man/figures/README-basic_coverage_protein-1.png

@@ -51,7 +51,7 @@ The goal of `ggcoverage` is simplify the process of visualizing omics coverage.
   * **peak annotation**: Visualize genome coverage and peak identified
   * **contact map annotation**: Visualize genome coverage with Hi-C contact map
   * **link annotation**: Visualize genome coverage with contacts
-  * **peotein feature annotation**: Visualize protein coverage with features
+  * **protein feature annotation**: Visualize protein coverage with features
 
 `ggcoverage` utilizes `ggplot2` plotting system, so its usage is **ggplot2-style**!
 
@@ -819,7 +819,7 @@ protein_coverage <- ggprotein(
 protein_coverage
 ```
 
-```{r basic_coverage_protein_plot, echo = FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein_plot, echo = FALSE, fig.height = 6, fig.width = 10, fig.align = "center"}
 knitr::include_graphics("../man/figures/README-basic_coverage_protein-1.png")
 ```
 
@@ -842,7 +842,7 @@ protein_coverage +
                feature.color = c("#4d81be", "#173b5e", "#6a521d"))
 ```
 
-```{r basic_coverage_protein_feature_plot, echo = FALSE, fig.height = 6, fig.width = 12, fig.align = "center"}
+```{r basic_coverage_protein_feature_plot, echo = FALSE, fig.height = 6, fig.width = 10, fig.align = "center"}
 knitr::include_graphics("../man/figures/README-basic_coverage_protein_feature-1.png")
 ```