plotHeatmapOfftargets: Plot offtargets from multiple samples as heatmap

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

Plot offtargets from multiple samples as heatmap

Description

Plot offtargets from multiple samples as heatmap

Usage

plotHeatmapOfftargets(
  mergedOfftargets,
  min.detection.rate = 0.1,
  font.size = 12,
  on.target.predicted.score = 1,
  IR.normalization = c("sequence.depth", "on.target.score", "sum.score", "none"),
  top.bottom.height.ratio = 3,
  dot.distance.breaks = c(5, 10, 20, 40, 60),
  dot.distance.scaling.factor = c(0.4, 0.6, 0.8, 1.2, 2),
  bottom.start.offset = 8,
  color.low = "white",
  color.high = "blue",
  sample.names,
  insertion.score.column = c("n.distinct.UMIs", "peak_score")
)

Arguments

mergedOfftargets	a data frame from running the combineOfftargets function
min.detection.rate	minimum relative detection rate to be included in the heatmap
font.size	font size for x labels and numbers along the y-axis.
on.target.predicted.score	Default to 1 for the CFDscore scoring method. Set it to 100 for the Hsu-Zhang scoring method.
IR.normalization	Default to sequence.depth which uses the sequencing depth for each sample in the input file to calculate the relative insertion rate (RIR). Other options are "on.target.score" and "sum.score" which use the on-target score for each sample and the sum of all on-target and off-target scores to calculate the RIR respectively. The score can be either peak.score or n.distinct.UMIs as specified by the parameter insertion.score.column
top.bottom.height.ratio	the ratio of the height of top panel vs that of the bottom panel.
dot.distance.breaks	a numeric vector for specifying the minimum number of rows in each panel to use the the corresponding distance in dot.distance.scaling.factor between consecutive dots along the y-axis. In the default setting, dot.distance.breaks and dot.distance.scaling.factor are set to c(5, 10, 20, 40, 60) and c(0.4, 0.6, 0.8, 1.2, 2) respectively, which means that if the number of rows in each panel is greater than or equal to 60, 40-59, 20-39, 10-19, 5-9, and less than 5,then the distance between consecutive dots will be plotted 2, 1.2, 0.8, 0,6, 0.4, and 0.2 (half of 0.4) units away in y-axis respectively.
dot.distance.scaling.factor	a numeric vector for specifing the distance between two consecutive dots. See dot.distance.breaks for more information.
bottom.start.offset	Default to 2, means that place the top number in the bottom panel 2 units below the top border. Increase the value will move the number away from the top border.
color.low	The color used to represent the lowest indel rate, default to white
color.high	The color used to represent the highest indel rate the intermediate indel rates will be colored using the color between color.low and color.high. Default to blue.
sample.names	Optional sample Names used to label the x-axis. If not provided, x-axis will be labeled using the sample names provided in the GUIDEseqAnalysis step.
insertion.score.column	"n.distinct.UMI" or "peak_score" to be included on the right side of the alignment as Insertion Events. Relative Insertion Rate (RIR) divided by ontarget peak_score/n.distinct.UMI. For example, RIR for ontarget should be 100

Value

a ggplot object

Author(s)

Lihua Julie Zhu

Examples

if (interactive())
{
  mergedOfftargets <- 
        read.table(system.file("extdata/forVisualization",
      "mergedOfftargets.txt",
       package = "GUIDEseq"),
                   sep ="\t", header = TRUE)
                   
 figs <- plotHeatmapOfftargets(mergedOfftargets,
                   min.detection.rate = 2.5,
                   IR.normalization = "on.target.score",
                   top.bottom.height.ratio = 12,
                   bottom.start.offset = 6,
                   dot.distance.scaling.factor = c(0.2,0.2,0.4,0.4, 0.4),
                   sample.names = c("Group1", "Group2"))
                   figs[[1]]/figs[[2]] +
 plot_layout(heights = unit(c(2,1),
                             c('null', 'null')))
                             
figs = plotHeatmapOfftargets(mergedOfftargets,
                 min.detection.rate = 1.2,
                 IR.normalization = "sum.score",
                 top.bottom.height.ratio = 12,
                 bottom.start.offset = 6,
                 dot.distance.scaling.factor = c(0.2,0.2,0.4,0.4, 0.4),
                 sample.names = c("Group1", "Group2"))
                 figs[[1]]/figs[[2]] +
                 plot_layout(heights = unit(c(2,1),
                  c('null', 'null')))
 figs <- plotHeatmapOfftargets(mergedOfftargets,
    min.detection.rate = 0.2,
    IR.normalization = "sequence.depth",
    top.bottom.height.ratio = 12,
    bottom.start.offset = 6,
    dot.distance.scaling.factor = c(0.2,0.2,0.2,0.2, 0.2),
    sample.names = c("Group1", "Group2"))
figs[[1]]/figs[[2]] +
    plot_layout(heights = unit(c(2,1),
    c('null', 'null')))
figs = plotHeatmapOfftargets(mergedOfftargets,
    min.detection.rate = 3,
    IR.normalization = "none",
    top.bottom.height.ratio = 12,
    bottom.start.offset = 6,
    dot.distance.scaling.factor = c(0.2,0.2,0.7,0.7, 0.7),
    sample.names = c("Group1", "Group2"))
    figs[[1]]/figs[[2]] 
plot_layout(heights = unit(c(2,1),
                c('null', 'null')))
}

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