- 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).