plot-IWTomicsData: Plot '"IWTomicsData"' object

In IWTomics: Interval-Wise Testing for Omics Data

Description

Method to plot objects of class "IWTomicsData". The function create graphical representations of the feature measurments in each region datasets, such as aligned curves, pointwise quantile curves, scatterplot and smoothed scatterplot.

Usage

## S4 method for signature 'IWTomicsData'
plot(x, type='boxplot',method='pearson',
  N_regions=pmin(lengthRegions(x),
                 ifelse(type=='curves',10,ifelse(type=='pairs',1000,+Inf))),
  probs=c(0.25,0.5,0.75), average=TRUE, size=TRUE,
  id_regions_subset=idRegions(x), id_features_subset=idFeatures(x),
  log_scale=FALSE, log_shift=0, col=1+seq_along(id_regions_subset),
  plot=TRUE, ask=TRUE, xlab='Windows', ylim=NULL,...)

Arguments

x	"IWTomicsData" object.
type	type of plot to be drawn. Possible types are: "boxplot" for the pointwise quantiles curves (default), "curves" for the (aligned) curves, "pairs" for the scatterplot matrix of the different features (same resolution needed), "pairsSmooth" for the smoothed scatterplot matrix of the different features (same resolution needed).
method	correlation coefficient to be computed and plotted if type="pairs" or type="pairsSmooth". Possible types are "pearson" (default), "kendall" and "spearman". See cor for details about the different methods.
N_regions	number of regions to be randomly chosen (for each region dataset) in "curves" and "pairs" type plot. Default plots a maximum of 10 and 1000 curves for "curves" and "pairs", respectively.
probs	probabilities corresponding to the quantiles to be drawn in "boxplot" type plot. Default plots quartile curves.
average	if TRUE, plot the mean curves.
size	if TRUE, plot the sample size in each position.
id_regions_subset	vector with the identifiers of the region datasets to be plotted.
id_features_subset	vector with the identifiers of the features to be plotted.
log_scale	plot the logarithm of the measurements.
log_shift	scalar with the shift to be applied before applying the logorithm, when log_scale=TRUE.
col	vector of plotting colors for the different region datasets. If type is "pairsSmooth", only the first element of col is used.
plot	it TRUE (default) a plot is drawn, otherwise a list of plot data is returned.
ask	if TRUE (default) the user is prompted before a new plot is drawn.
xlab	a title for the x axis.
ylim	the y limits of the plot.
...	additional plot parameters.

Value

plot returns a list with components depending on the plot type.

If type is "pairs" or "pairsSmooth" the list has components:

features_plot	matrix with the data plotted, one column for each feature considered.
features_cor	correlation matrix.
type	type of plot drawn.

If type is "boxplot" or "curves" the list has components:

x_plot	a list of vectors with the abscissa for each feature.
features_plot	if type is "boxplot", a list of matrix lists with the data plotted for each feature and each region datasets. Each column represents one quantile drawn. If type is "curves", a list of matrices with the data plotted for each feature. Each column represents one curve drawn.
features_average	if average is TRUE, a list of matrices with the average curves for each feature. Each column represents the average curve for a region dataset.
features_position_size	if size is TRUE, a list of matrices with the sample size for each feature. Each column represents the sample size in each position for a region dataset.
type	type of plot drawn.
col	vector of plotting colors for the different region datasets.
col_plot	if type is "boxplot", list of plotting colors for each feature (quantile curves colors and shaded band colors). If type is "curves", vector of plotting colors correspondent to the different curves in features_plot.

Author(s)

Marzia A Cremona, Alessia Pini, Francesca Chiaromonte, Simone Vantini

See Also

IWTomicsData for "IWTomicsData" class, constructors, accessors and methods; smooth method to smooth curves in "IWTomicsData" objects; IWTomicsTest for the Interval-Wise Testing.

Examples

data(regionsFeatures_center)

## Plot the pointwise boxplot of the curves in the different region datasets
plot(regionsFeatures_center,type='boxplot')

## Plot all the curves in the different region datasets
plot(regionsFeatures_center,type='curves',N_regions=lengthRegions(regionsFeatures_center))

## Scatterplot of the measurements in the different region datasets
plot(regionsFeatures_center,type='pairs',N_regions=lengthRegions(regionsFeatures_center))

## Smooth scatterplot of the measurements in the 'control' region datasets
plot(regionsFeatures_center,type='pairsSmooth',id_regions_subset='control',
     N_regions=lengthRegions(regionsFeatures_center)['control'],col=5)

IWTomics documentation built on Nov. 8, 2020, 5:33 p.m.