SNPhood (version 1.2.3)

plotRegionCounts: Visualize the raw read counts across regions or a user-defined genomic range

Description

plotBinCounts visualizes the raw read counts (i.e., before binning user regions) across regions or a user-defined genomic range. Note that only the results of a particular chromosome can be visualized. It is therefore only possible if the regions to be visualized are located on one particular chromosome; otherwise, an error is thrown.

Usage

plotRegionCounts(SNPhood.o, regions = NULL, datasets = NULL, readGroups = NULL, mergeReadGroupCounts = FALSE, plotChr = NULL, plotStartPos = NULL, plotEndPos = NULL, ylim = NULL, plotRegionBoundaries = FALSE, plotRegionLabels = FALSE, maxWidthLabels = NULL, colorPalette = "Set1", sizePoints = 4, type = "p", plotGraph = TRUE, fileToPlot = NULL, verbose = FALSE)

Arguments

SNPhood.o

Object of class SNPhood

regions

Numeric or Character or NULL. Default NULL. Regions that should be plotted, either specified as integer (such as 1, value must be between 1 and the total number of regions as defined in the object) or their annotation (name must appear in the region names as obtained via the function annotationRegions). If set to NULL, all regions will be considered.

datasets

Numeric or Character or NULL. Default NULL. Datasets that should be used for plotting, either specified as integer (such as 1, value must be between 1 and the total number of datasets as defined in the object) or their annotation (name must appear in the dataset names as obtained via the function annotationDatasets). If set to NULL, all datasets will be considered.

readGroups

Character or NULL. Default NULL. Read groups that should be plotted, specified by their name as obtained by the function annotationReadGroups). If set to NULL, all read groups will be considered.

mergeReadGroupCounts

Logical(1). Default FALSE. Should the read groups be merged for visualization purposes?

plotChr

Character(1) or NULL. Default NULL. The name of the chromosome for which the visualization should be done. Must be a valid chromosome name. If set to NULL, other parameters (such asregions) determine which genomic region should be plotted.

plotStartPos

Character(1) or NULL. Default NULL. The start coordinates for which the visualization should be done. Must be a valid number with respect to the chromosome it refers to. If set to NULL and the parameter plotChr is not NULL, the start coordinates are set to 1.

plotEndPos

Character(1) or NULL. Default NULL. The end coordinates for which the visualization should be done. Must be a valid number with respect to the chromosome it refers to. If set to NULL and the parameter plotChr is not NULL, the end coordinates are determined automatically and the full chromosome will be plotted.

ylim

Numeric(2). Default NULL. Range of the y-axis, as specified by a minimum and a maximum value. See ?ylim for details.

plotRegionBoundaries

Logical(1). Default FALSE. Should the region boundaries be drawn in the plot? If set to TRUE, two vertical lines will be drawn for each region, corresponding to the region boundaries upstream and downstream of the SNP. This visual aid may help to judge the size of the regions and overlaps among regions.

plotRegionLabels

Logical(1). Should the annotation of the regions be drawn vertically below the x axis? If many regions are plotted, labels may overlap; however, for a few regions, this is usually not a problem.

maxWidthLabels

Numeric(1). Default NULL. Maximum width of the legend labels in number of characters. If the width of the legend labels are longer, they are shortened. Set to NULL to not shorten labels.

colorPalette

Character(1). Default "Set1". Name of the palette from the RColorBrewer package from the qualitative palettes for the colors of the datasets that are plotted. Allowed palette names are "Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", and "Set3". Colors for the datasets are then determined automatically from the given palette name (from left to right, depending on the number of datasets to be plotted). The colors for the read groups within each datasets are based on the colors for the dataset, but with different saturation values.

sizePoints

Numeric(1). Default 4. Size of the points that are drawn in the plot (if type is set to the default value of "p"). This parameter has no effect if type is set to "l".

type

Character(1). "p" or "l". Default "p". What type of plot should be drawn, points ("p") or lines ("l")?

plotGraph

Logical(1). Default TRUE. Should the graphs be plotted to the current graphics device?

fileToPlot

Character(1) or NULL. Default NULL. Filename of the PDF file for the output plots. If set to NULL, plots will be plotted to the currently active device.

verbose

Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

the generated ggplot2 plot(s) as list for further processing. May contain multiple plots, depending on the function. The plot(s) can then be plotted individually or modified arbitrarily as the user wants. For example, if multiple plots are returned and the plots have been saved in a variable called plots.l, simply type plots.l[[1]] to view the first plot.

Examples

data(SNPhood.o, package="SNPhood")

# Plot the read counts for the first ten regions
plot = plotRegionCounts(SNPhood.o, regions = 1:10)

# Plot the read counts for the full chr21
plot = plotRegionCounts(SNPhood.o, plotChr = "chr21")

# Plot the read counts for the full chr21, merge read group counts and decrease the point size
plot = plotRegionCounts(SNPhood.o, plotChr = "chr21", sizePoints = 2, mergeReadGroupCounts = TRUE)