plotFeatures-methods: plotFeatures

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Visualize the relations between predictors and response variable ('tssOverlap').

Usage

1
2
3
4
5
6
plotFeatures(object, plot.type = c("box", "density"), feature, ncol, xlab,
  ylab, color = c("#E41A1C", "#377EB8"), alpha = 1)

## S4 method for signature 'ChipDataSet'
plotFeatures(object, plot.type = c("box", "density"),
  feature, ncol, xlab, ylab, color = c("#E41A1C", "#377EB8"), alpha = 1)

Arguments

object

A ChipDataSet object.

plot.type

One of ["box", "density"]. Default: "box"

feature

Feature to plot. By default, all the features are plotted.

ncol

Numeric. Arrange individual plots in columns. By default, the number of columns correspond to the number of features used for plotting.

xlab

Character. Title of the x-axis

ylab

Character. Title of the y-axis.

color

A character vector of length two. Default: ["#E41A1C","#377EB8"].

alpha

Color transparency. In a range [0, 1]. Default: 1.

Details

In order to discriminate between functional or gene associated peaks and non-functional or background peaks, each peak in the data set is characterized by several features. Moreover, the user might supply her/his own list of features with the addFeature. Prior to fitting the logistic model, the relations between predictors and response variable (tssOverlap) can be explored with plotFeatures. Based on the plots, poor predictors can be excluded from the analysis to improve the model fit.

Value

ggplot2 object.

Author(s)

Armen R. Karapetyan

See Also

constructCDS

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
### Load ChipDataSet object
data(cds)

### The data can be plotted in two ways
### As a boxplot
plotFeatures(object = cds, plot.type = "box")

### Or as a density plot
plotFeatures(object = cds, plot.type = "density")

### Additionally, only the subset of features can be shown
plotFeatures(object = cds, plot.type = "box", feature = c("pileup", "length"))

### The position of the graphs on the plot, can be adjusted by 'ncol' argument
plotFeatures(object = cds, plot.type = "box", ncol = 2)


Search within the transcriptR package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.