plotGenome | R Documentation |
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.
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" )
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). |
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
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