plotGenome {Repliscope}

plotGenome: plot replication profile.

Description

plotGenome plots scatterplot/barplot/polygon of 'score' and/or 'splineSmooth' columns values by genomic coordinates, either for the whole genome or a region. It also allows annotation with additional BED-formatted data. Ggplot2 package is used for plotting.

Usage

plotGenome(
  ratioDFs,
  geom = "geom_point",
  ylims = c(1, 2),
  plotting = TRUE,
  genome = NULL,
  region = FALSE,
  guide = NULL,
  lines = NULL,
  circles = NULL,
  rectangles = NULL,
  pointers = NULL,
  colourLines = "#00FF00",
  colourCircles = "#FFFFFF",
  colourRectangles = "#FF0000",
  colourPointers = "#FF7F00"
)

Arguments

ratioDFs

A ratio dataframe or combined ratios dataframe containing 'ratio' column (dataframe).

geom

ggplot2 geom to use for plotting: "geom_point","geom_ribbon" or "geom_segment" (string, defaults to "geom_point").

ylims

A vector of two values for y axis limits - first is lowest, second is highest (numeric vector, defaults to 1 and 2)

plotting

Should the plot object be sent to the default device? (boolean, defaults to TRUE).

genome

A mask dataframe to exclude data from the ratio dataframe (dataframe, optional). The genome dataframe must contain "chrom","chromStart" and "chromEnd" columns.

region

Only plot for the provided region in the format 'chrI:1000-3000' (string, optional).

guide

A dataframe guiding the plotGenome function how to plot the data (dataframe, optional). The guide dataframe must contain the following columns: 'order' (integer) - order to plot data in, 'name.rep' (character) - replicating sample name that matches the one in the ratioDFs dataframe, 'name.nonRep' (character) - non-replicating sample name that matches the one in the ratioDFs dataframe, 'raw' (logical) - should the raw raw data be plotted? 'smooth' (logical) - should the smoothed data be plotted? 'color'(character) - R color to plot the current sample with, both raw and smoothed data.

lines

Additionally plot vertical lines from a BED formatted dataframe (dataframe, optional).

circles

Additionally plot circles on the chromosome line from a BED formatted dataframe (dataframe, optional).

rectangles

Additionally plot rectangles on the chromosome line from a BED formatted dataframe (dataframe, optional).

pointers

Additionally plot downward pointing triangles from a BED formatted dataframe (dataframe, optional).

colourLines

Colour for 'lines' data (string, defaults to green).

colourCircles

Colour for 'circles' data (string, defaults to white).

colourRectangles

Colour for 'rectangles' data (string, defaults to red).

colourPointers

Colour for 'pointers' data (string, defaults to orange).

Examples

plotGenome(sortSeq,geom="geom_ribbon",guide=guide,region="chrIX:250000-439885",
    lines=sacCer3[["cen"]],circles=sacCer3[["ori"]])
# plot data as polygon for the specified region of chromosome 9

plotGenome(syncSeq[["data"]],geom="geom_segment",guide=syncSeq[["guide"]],
    region="chrVII:0-1090944",genome=sacCer3[["genome"]],lines=sacCer3[["cen"]],
    circles=sacCer3[["ori"]],colourLines="black")

plotGenome(MFAseq,region='chr1:0-2848000')
# plot marker frequency analysis for H.volcanii isolate DS2