feat: removed 11 strict dependencies, refactored many functions to wo…

…rk with basic solutions; closes #27, related to #29

DESCRIPTION

@@ -23,40 +23,32 @@ BugReports: https://github.com/showteeth/ggcoverage/issues
 Imports: 
     BiocParallel,
     Biostrings,
-    BSgenome,
     dplyr,
     GenomeInfoDb,
     GenomicAlignments,
     GenomicRanges,
-    ggbio,
-    ggforce,
     ggh4x,
     ggpattern,
     ggplot2,
     ggrepel,
     grDevices,
     gridExtra,
-    HiCBricks,
     IRanges,
-    magrittr,
     methods,
-    openxlsx,
     patchwork,
-    RColorBrewer,
-    reshape2,
     rlang,
     Rsamtools,
     rtracklayer,
-    S4Vectors,
     scales,
-    seqinr,
     stats,
-    stringr,
     utils
 Suggests: 
     BiocStyle,
     BSgenome.Hsapiens.UCSC.hg19,
+    ggbio,
+    ggforce,
     graphics,
+    HiCBricks,
     HiCDataHumanIMR90,
     htmltools,
     knitr,

NAMESPACE

@@ -46,14 +46,14 @@ export(theme_protein2)
 export(theme_tad)
 export(theme_tad2)
 export(theme_transcript)
-import(HiCBricks)
-importFrom(BSgenome,getSeq)
 importFrom(BiocParallel,MulticoreParam)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,register)
+importFrom(Biostrings,getSeq)
 importFrom(Biostrings,letterFrequency)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,readDNAStringSet)
+importFrom(Biostrings,translate)
 importFrom(GenomeInfoDb,"seqlengths<-")
 importFrom(GenomeInfoDb,seqlengths)
 importFrom(GenomeInfoDb,seqnames)
@@ -70,10 +70,9 @@ importFrom(GenomicRanges,trim)
 importFrom(IRanges,IRanges)
 importFrom(IRanges,findOverlaps)
 importFrom(IRanges,subsetByOverlaps)
-importFrom(RColorBrewer,brewer.pal)
 importFrom(Rsamtools,ScanBamParam)
 importFrom(Rsamtools,indexBam)
-importFrom(S4Vectors,"values<-")
+importFrom(dplyr,"%>%")
 importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
@@ -82,8 +81,6 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
-importFrom(ggbio,layout_karyogram)
-importFrom(ggforce,geom_bezier)
 importFrom(ggh4x,elem_list_rect)
 importFrom(ggh4x,facet_wrap2)
 importFrom(ggh4x,strip_themed)
@@ -100,6 +97,7 @@ importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expansion)
 importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_curve)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_label)
 importFrom(ggplot2,geom_line)
@@ -115,7 +113,7 @@ importFrom(ggplot2,ggplot_add)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,rel)
-importFrom(ggplot2,scale_color_gradient2)
+importFrom(ggplot2,scale_color_gradientn)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_x_continuous)
@@ -129,20 +127,16 @@ importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,grey)
 importFrom(gridExtra,tableGrob)
 importFrom(gridExtra,ttheme_default)
-importFrom(magrittr,"%>%")
 importFrom(methods,extends)
-importFrom(openxlsx,read.xlsx)
 importFrom(patchwork,wrap_plots)
-importFrom(reshape2,melt)
 importFrom(rlang,.data)
 importFrom(rlang,as_label)
 importFrom(rtracklayer,import)
 importFrom(scales,comma)
 importFrom(scales,rescale)
 importFrom(scales,scientific)
-importFrom(seqinr,translate)
 importFrom(stats,as.formula)
-importFrom(stringr,str_locate)
+importFrom(stats,reshape)
 importFrom(utils,menu)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)

R/FormatInput.R

@@ -41,7 +41,7 @@ GetRegion <- function(df, chr, start, end = NULL) {
 #' @param extend Extend length of \code{region}. Default: 2000.
 #'
 #' @return A dataframe.
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #' @importFrom dplyr filter arrange
 #'
 #' @export

R/LoadTrack.R

@@ -31,7 +31,7 @@
 #' @importFrom GenomicAlignments alphabetFrequencyFromBam readGAlignments coverage
 #' @importFrom GenomicRanges GRanges
 #' @importFrom IRanges IRanges subsetByOverlaps
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #' @importFrom dplyr select filter mutate all_of group_by summarize
 #' @importFrom BiocParallel register MulticoreParam bplapply
 #' @importFrom ggplot2 cut_width