add revNegStrand parameters

R/trancriptVis.R

@@ -50,10 +50,11 @@
 #' @param strip.position Facet plot strip.position, same as "facet_wrap" function, default('top').
 #' @param forcePosRel Whether force the genome coordinate to relative position to transcript start/end position, default('FALSE').
 #' @param panel.spacing Facet plot panel space, default(0.3).
+#' @param revNegStrand Whether reverse the negtive strand when set "forcePosRel=TRUE", default('FALSE').
 #'
 #' @import tidyverse
 #'
-#' @return ggplot object.
+#' @return A ggplot object.
 #'
 #' @export
 #' @examples
@@ -186,7 +187,8 @@ trancriptVis <- function(gtfFile = NULL,
  scales = 'free',
  strip.position = 'top',
  forcePosRel = FALSE,
- panel.spacing = 0.3){
+ panel.spacing = 0.3,
+ revNegStrand = FALSE){
  ##############################################################################
  # test whether with a given specific gene or region
  if(is.null(gene)){
@@ -264,12 +266,31 @@ trancriptVis <- function(gtfFile = NULL,
  tmp1 <- tmp %>% dplyr::filter(transcript_id == t) %>%
  dplyr::arrange(start,end)
 
- # start coord
- startPos <- tmp1$start[1]
+ # whether reverse negtive strand
+ if(revNegStrand == FALSE){
+ # start coord
+ startPos <- min(tmp1$start)
 
- # add new pos
- tmp1 <- tmp1 %>% dplyr::mutate(start = start - startPos,
- end = end - startPos)
+ # add new pos
+ tmp1 <- tmp1 %>% dplyr::mutate(start = start - startPos,
+ end = end - startPos)
+ }else{
+ if(unique(tmp1$strand) == '-'){
+ # end coord
+ endPos <- max(tmp1$end)
+
+ # add new pos
+ tmp1 <- tmp1 %>% dplyr::mutate(start = endPos - start,
+ end = endPos - end)
+ }else{
+ # start coord
+ startPos <- min(tmp1$start)
+
+ # add new pos
+ tmp1 <- tmp1 %>% dplyr::mutate(start = start - startPos,
+ end = end - startPos)
+ }
+ }
  return(tmp1)
  }) -> relPos_tmp
  return(relPos_tmp)
@@ -284,9 +305,14 @@ trancriptVis <- function(gtfFile = NULL,
  trans <- exonNewPos %>% dplyr::filter(type == 'transcript')
 
  # add text x/y pos
- trans$textX <- ifelse(trans$strand == '+',trans$start + trans$width/2,
- trans$end - trans$width/2)
- trans$textY <- trans$yPos + relTextDist
+ if(revNegStrand == FALSE){
+ trans$textX <- ifelse(trans$strand == '+',trans$start + trans$width/2,
+ trans$end - trans$width/2)
+ trans$textY <- trans$yPos + relTextDist
+ }else{
+ trans$textX <- (trans$start + trans$end)/2
+ trans$textY <- trans$yPos + relTextDist
+ }
 
  ##############################################################################
  # whether add specific arrow
@@ -339,6 +365,13 @@ trancriptVis <- function(gtfFile = NULL,
  }) -> arrow_trans
  }
 
+ # change reversed specArrow direction
+ if(revNegStrand == FALSE){
+ arrow_trans <- arrow_trans
+ }else{
+ arrow_trans$vl_x2 <- abs(arrow_trans$vl_x2)
+ }
+
  # strand control arrow direction
  arrow_trans$ad <- ifelse(arrow_trans$strand == '+','last','first')