plotTracks: Plot offtargets as manhantann plots or along all chromosomes...

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Plot offtargets as manhantann plots or along all chromosomes with one track per chromosome, or scatter plot for two selected measurements

Description

Plot offtargets as manhantann plots or along all chromosomes with one track per chromosome, or scatter plot for two selected measurements

Usage

plotTracks(
  offTargetFile,
  sep = "\t",
  header = TRUE,
  gRNA.size = 20L,
  PAM.size = 3L,
  cleavage.position = 19L,
  chromosome.order = paste0("chr", c(1:22, "X", "Y", "M")),
  xlab = "Chromosome Size (bp)",
  ylab = "Peak Score",
  score.col = c("peak_score", "n.distinct.UMIs", "total.match", "gRNA.match",
    "total.mismatch.bulge", "gRNA.mismatch.bulge", "predicted_cleavage_score"),
  transformation = c("log10", "none"),
  title = "",
  axis.title.size = 12,
  axis.label.size = 8,
  strip.text.y.size = 9,
  off.target.line.size = 0.6,
  on.target.line.size = 1,
  on.target.score = 1,
  on.target.color = "red",
  off.target.color = "black",
  strip.text.y.angle = 0,
  scale.grid = c("free_x", "fixed", "free", "free_y"),
  plot.type = c("manhattan", "tracks", "scatter"),
  family = "serif",
  x.sep = 6e+06,
  plot.zero.logscale = 1e-08,
  scale.chrom = TRUE
)

Arguments

offTargetFile	The file path containing off-targets generated from GUIDEseqAnalysis
sep	The separator in the file, default to tab-delimited
header	Indicates whether the input file contains a header, default to TRUE
gRNA.size	The size of the gRNA, default 20
PAM.size	PAM length, default 3
cleavage.position	the cleavage position of Cas nuclease, default to 19 for SpCas9.
chromosome.order	The chromosome order to plot from top to bottom
xlab	The x-asix label, default to Chromosome Size (bp)
ylab	The y-asix label, default to Peak Score. Change it to be consistent with the score.col
score.col	The column used as y values in the plot. Available choices are peak_score, n.distinct.UMIs, total.match, gRNA.match, total.mismatch.bulge, gRNA.mismatch.bulge, and predicted_cleavage_score. When plot.type is set to scatter, a vector of size two can be set. Otherwise, a scatter plot with log10 transformed n.distinct.UMIs and log10 transformed predicted_cleavage_score will be plotted.
transformation	Indicates whether plot the y-value in log10 scale or in the original scale. When scale.col is set to total.match, gRNA.match, total.mismatch.bulge, and gRNA.mismatch.bulge, transformation will not be applied and the data will be plotted in the original scale. When plot.type is set to "scatter", a vector of size two is required when score.col is a vector of size two. Examples are c("log10", "log10"), c("none", "none"), c(log10", "none"), and c("none", "log10").
title	The figure title, default to none.
axis.title.size	The font size for the axis labels, default to 12
axis.label.size	The font size for the tick labels, default to 8
strip.text.y.size	The font size for the strip labels, default to 9
off.target.line.size	The line size to depict the off-targets, default to 0.6
on.target.line.size	The line size to depict the on-targets, default to 1
on.target.score	The score for the on-target, default to 1 for CFD scoring system. This is the maximum score in the chosen scoring system. Change it accordingly if different off-target scoring system is used.
on.target.color	The line color to depict the on-targets, default to red
off.target.color	The line color to depict the off-targets, default to black
strip.text.y.angle	The angel for the y strip text, default to 0. Set it to 45 if angled representation is desired
scale.grid	Used to set the scales in facet_grid, default to free_x, meaning that scales vary across different x-axis, but fixed in y-axis. Other options are fixed, free, and free_y meaning that scales shared across all facets, vary across both x- and y- axises, and vary across y-axis only, respectively. For details, please type ?ggplot2::facet_grid
plot.type	Plot type as tracks by individual chromosome or manhattan plot with all chromosome in one plot
family	font family, default to sans (Arial). Other options are serif (Times New Roman) and mono (Courier). It is possible to use custom fonts with the extrafont package with the following commands install.packages("extrafont") library(extrafont) font_import() loadfonts(device = "postscript")
x.sep	For transforming the x-axis to allow sufficient spaces between small chromosomes default to 6000000
plot.zero.logscale	Specifying "none" to filter out score.col with zeros when plotting in log10 scale. Specify a very small numeric number if you intend to show the zeros in log scale in the figure. If users specify a number that's bigger than any positive score, plot.zero.logscale will be set to the minimum positive score divided by 10.
scale.chrom	Applicable to manhatann plot only. TRUE or FALSE default to TRUE to space offtargets evenly along x-axis.

Value

a ggplot object

Author(s)

Lihua Julie Zhu

Examples

if (interactive())
{
   offTargetFilePath <- system.file("extdata/forVisualization",
      "offTargetsInPeakRegions.xls",
       package = "GUIDEseq")
  fig1 <- plotTracks(offTargetFile = offTargetFilePath)
  fig1
  fig2 <- plotTracks(offTargetFile = offTargetFilePath,
    score.col = "total.mismatch.bulge",
    ylab = "Total Number of Mismatches and Bulges")
  fig2
  fig3 <- plotTracks(offTargetFile = offTargetFilePath,
     score.col = "total.match",
     ylab = "Total Number of Matches")
  fig3
  fig4 <- plotTracks(offTargetFile = offTargetFilePath,
      score.col = "gRNA.match",
      ylab = "Number of Matches in gRNA")
  fig4
  fig5 <- plotTracks(offTargetFile = offTargetFilePath,
      score.col = "gRNA.mismatch.bulge",
      ylab = "Number of Mismatches and Bulges in gRNA")
  fig5
  fig6 <- plotTracks(offTargetFile = offTargetFilePath,
     score.col = "predicted_cleavage_score",
     ylab = "CFD Score",
     scale.grid = "fixed",
     transformation = "none")
 fig6
 
 ## manhattan plot
  fig <- plotTracks(offTargetFile = offTargetFilePath,
        score.col = "total.mismatch.bulge", axis.title.size =9,
        plot.type =  "manhattan",
        ylab = "Number of Mismatches and Bulges in gRNA Plus PAM")
   fig
  fig <- plotTracks(offTargetFile = offTargetFilePath,
       score.col = "total.match", axis.title.size =9,
       plot.type =  "manhattan",
       ylab = "Number of Matches in gRNA Plus PAM")
   fig
fig <- plotTracks(offTargetFile = offTargetFilePath,
                 score.col = "gRNA.match",axis.title.size =9,
                 plot.type =  "manhattan",
                 ylab = "Number of Matches in gRNA")
fig
fig <- plotTracks(offTargetFile = offTargetFilePath,
                 score.col = "gRNA.mismatch.bulge", axis.title.size =9, 
                 plot.type =  "manhattan",
                 ylab = "Number of Mismatches and Bulges in gRNA")
  fig
  
  plotTracks(offTargetFile = offTargetFilePath,
      #'score.col = "predicted_cleavage_score",
      axis.title.size =9, family = "serif", plot.zero.logscale = 1e-6,
      plot.type =  "manhattan", transformation = "log10",
      ylab = "CFD Score")
      
  plotTracks(offTargetFile = offTargetFilePath,
       score.col = "peak_score",
       axis.title.size =9, 
       plot.type =  "manhattan",
       ylab = "Number of Insertion Events")
       
  plotTracks(offTargetFile = offTargetFilePath,
       score.col = "n.distinct.UMIs",
       axis.title.size =9, 
       plot.type =  "manhattan",
       ylab = "Number of Insertion Events")
       
 # default scatter plot with blue line from fitting the entire dataset
 # and the red line from fitting the subset with CFD score > 0
  plotTracks(offTargetFile = offTargetFilePath,
      axis.title.size =9, plot.zero.logscale = 1e-8,
      plot.type =  "scatter")
      
 # select the x, y, the transformation of x and y,
 # and the labels on the scatter plot
 
  plotTracks(offTargetFile = offTargetFilePath,
      axis.title.size =9,
      score.col = c("n.distinct.UMIs", "predicted_cleavage_score"), 
      transformation = c("log10", "log10"),
      plot.type =  "scatter", plot.zero.logscale = 1e-8,
      xlab = "log10(Number of Insertion Events)",
      ylab = "log10(CFD score)")
       
 }

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.