plotAlignedOfftargets: Plot offtargets aligned to the target sequence

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

Plot offtargets aligned to the target sequence

Description

Plot offtargets aligned to the target sequence

Usage

plotAlignedOfftargets(
  offTargetFile,
  sep = "\t",
  header = TRUE,
  gRNA.size = 20L,
  input.DNA.bulge.symbol = "^",
  input.RNA.bulge.symbol = "-",
  input.match.symbol = ".",
  plot.DNA.bulge.symbol = "DNA.bulge",
  plot.RNA.bulge.symbol = "-",
  plot.match.symbol = ".",
  color.DNA.bulge = "red",
  size.symbol = 3,
  color.values = c(A = "#B5D33D", T = "#AE9CD6", C = "#6CA2EA", G = "#FED23F", `-` =
    "gray", . = "white"),
  PAM = "GGG",
  body.tile.height = 2.5,
  header.tile.height = 3.6,
  hline.offset = 3.8,
  plot.top.n,
  insertion.score.column = c("n.distinct.UMIs", "peak_score"),
  insertion.score.column.prefix,
  width.IR = 2.5,
  width.RIR = 2.5,
  family = "sans",
  hjust = "middle",
  vjust = 0.5
)

Arguments

offTargetFile	The path of the file offTargetsInPeakRegions.xls that stores the offtargets to be plotted. This file is the output file from the function GUIDEseqAnalysis.
sep	Field delimiter for the file specified as offTargetFile, default to tab dilimiter
header	Indicates whether there is header in the file specified as offTargetFile, default to TRUE
gRNA.size	Size of the gRNA, default to 20 for SpCas9 system
input.DNA.bulge.symbol	The symbol used to represent DNA bulges in the file specified as offTargetFile, default to "^"
input.RNA.bulge.symbol	The symbol used to represent RNA bulges in the file specified as offTargetFile, default to "-"
input.match.symbol	The symbol used to represent matched bases in the file specified as offTargetFile, default to "."
plot.DNA.bulge.symbol	The symbol used to represent DNA bulges in the figure to be generated, default to DNA.bulge, i.e., the nucleotide in the DNA bulge. Alternatively, you can specify a symbol to represent all DNA bulges such as "I".
plot.RNA.bulge.symbol	The symbol used to represent RNA bulges in the figure to be generated, default to "-"
plot.match.symbol	The symbol used to represent matched bases in the figure to be generated, default to "."
color.DNA.bulge	The color used to represent DNA bulges in the figure to be generated, default to "red"
size.symbol	The size used to plot the bases, and the symbols of DNA/RNA bulges, default to 3
color.values	The color used to represent different bases, DNA bulges, and RNA bulges.
PAM	PAM sequence in the target site, please update it to the exact PAM sequence in the input target site.
body.tile.height	Specifies the height of each plotting tile around each base/symbol for offtargets, default to 2.5
header.tile.height	Specifies the height of each plotting tile around each base/symbol for the target sequence on the very top, default to 3.6
hline.offset	Specifies the offset from the top border to draw the horizontal line below the gRNA sequence, default to 3.8. Increase it to move the line down and decrease it to move the line up.
plot.top.n	Optional. If not specified, all the offtargets in the input file specified as offTargetFile will be included in the plot. With a very large number of offtargets, users can select the top n offtargets to be included in the plot. For example, set plot.top.n = 20 to include only top 20 offtargets in the plot. Please note offtargets are ordered by the n.distinct.UMIs or peak_score from top to bottom.
insertion.score.column	"n.distinct.UMIs" or "peak_score" to be included on
insertion.score.column.prefix	to designate sample name e.g., S1 which means that two of columns are named as S1.peak_score and S1.n.distinct.UMIs in the input file. Useful if the input file is generated by the function combineOfftargets the right side of the alignment as Insertion Events. Relative Insertion Rate (RIR) divided by ontarget peak_score/n.distinct.UMIs. For example, RIR for ontarget should be 100
width.IR	For adjusting the width of the IR output
width.RIR	For adjusting the width of the RIR output
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")
hjust	horizontal alignment
vjust	vertical alignment

Value

a ggplot object

Author(s)

Lihua Julie Zhu

Examples

offTargetFilePath <- system.file("extdata/forVisualization",
 "offTargetsInPeakRegions.xls",
 package = "GUIDEseq")
fig1 <- plotAlignedOfftargets(offTargetFile = offTargetFilePath,
    plot.top.n = 20,
    plot.match.symbol = ".",  
    plot.RNA.bulge.symbol = "-", 
    insertion.score.column = "peak_score")
fig1

fig2 <- plotAlignedOfftargets(offTargetFile = offTargetFilePath,
    plot.top.n = 20,
    plot.match.symbol = ".",  
    plot.RNA.bulge.symbol = "-", 
    insertion.score.column = "n.distinct.UMIs")
fig2

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