BlastCoordPlotly: Compute the elements that represent the blast configuration...

In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline

Description

Compute the elements that represent the blast configuration for a interactive plotly graph

Usage

BlastCoordPlotly(
  QuerySeqId,
  QueryLength,
  QueryStart,
  QueryEnd,
  SubjectSeqId,
  SubjectStart,
  SubjectEnd,
  SubjectLength,
  Length,
  Height = 0.5,
  Step = 10,
  LineDots = 100
)

Arguments

QuerySeqId	Name of the query (submitted sequence)
QueryLength	Length of the query (full length not the mapped part)
QueryStart	Beggining postition of the matching part in the query
QueryEnd	Ending position of the matching part in the query
SubjectSeqId	Name of the subject (reference sequence)
SubjectStart	Beggining postition of the matching part in the subject
SubjectEnd	Ending position of the matching part in the subject
SubjectLength	Length of the query (full length not the mapped part)
Length	Length of the matching part between subject and query
Height	height of the widget
Step	fraction of the gap between the shared parts and the specific parts
LineDots	inneer graduation set in AA

Value

List of Dataframes for a plotly graph

Examples

library(plotly)
library(viridisLite)
BlastPalette<-viridis(3)
R_FilePath <- system.file("extdata",
 "blast_rescue.example.txt",
  package = "isoformnspectRe")
Rescue<-read.table(
 R_FilePath,
 header=TRUE)
 Infos <- Rescue[1,]
 DFs <- BlastCoordPlotly(Infos$QuerySeqId, Infos$QueryLength, Infos$QueryStart,
 Infos$QueryEnd, Infos$SubjectSeqId, Infos$SubjectStart, Infos$SubjectEnd,
 Infos$SubjectLength, Infos$Length)
 names(BlastPalette) <- c(as.vector(Infos$QuerySeqId) ,
 paste( as.vector(Infos$QuerySeqId), "<br>", as.vector(Infos$SubjectSeqId), sep = "" ),
 as.vector(Infos$SubjectSeqId))
 P<-plotly::plot_ly()
 P <- plotly::add_trace(P,
 x = DFs$MatchBlock$x,
 y = DFs$MatchBlock$y,
 color = I(as.vector(BlastPalette[2])), type = "scatter", mode = "lines",
 fill = "toself", name = paste( as.vector(Infos$QuerySeqId), "<br>",
 as.vector(Infos$SubjectSeqId), sep = ""), hoverinfo="name",hoverlabel=list(namelength=-1))
 P
 P <- plotly::add_trace(P, x = DFs$SubjectBlock$x, y = DFs$SubjectBlock$y,
 color = I(as.vector(BlastPalette[3])), type = "scatter", mode = "lines", fill = "toself",
 name = Infos$SubjectSeqId, hoverinfo="name", hoverlabel=list(namelength=-1))
 P
 P <- plotly::add_trace(P, x = DFs$QueryBlock$x, y = DFs$QueryBlock$y,
 color = I(as.vector(BlastPalette[1])), type = "scatter", mode = "lines", fill = "toself",
  name = Infos$SubjectSeqId,
 hoverinfo="name", hoverlabel=list(namelength=-1))
 P
 P<-plotly::add_segments(P, x=~x, y=~y, xend=~xend, yend=~yend,
 hoverinfo="text", color=I(BlastPalette[3]), text=~text,
 data=DFs$SubjectConnectors)
 P
 P<-plotly::add_segments(P, x=~x, y=~y, xend=~xend, yend=~yend,
 hoverinfo="text", color=I(BlastPalette[1]), text=~text,
 data=DFs$QueryConnectors)
 P
 P<-plotly::hide_legend(P)
 P

47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.