plotTest {IWTomics} | R Documentation

## Detailed plots of Interval-Wise Testing result

### Description

The function `plotTest` creates graphical representations of the Interval-Wise Testing results present in the `test` slot of a `"IWTomicsData"` object. In particular, it draws a heatmap of the adjusted p-value functions at each possible scale (with the different maximum interval lengths considered), a plot of the adjusted p-value curve at the chosen scale threshold and a plot of the feature measurements in the region datasets tested (aligned curves or pointwise quantile curves).

### Usage

    plotTest(regionsFeatures, alpha=0.05, scale_threshold=NULL, nlevel=100, type="boxplot",
      N_regions=pmin(lengthRegions(regionsFeatures),10),
      probs=c(0.25,0.5,0.75), average=TRUE, size=TRUE,
      id_features_subset=idFeatures(regionsFeatures),
      col=1+seq_len(nRegions(regionsFeatures)),
      ask=TRUE, xlab="Windows", ylim=NULL, ...)

### Arguments

`regionsFeatures` | `"IWTomicsData"` object with `test` slot.
`alpha` | level of the hypothesis test used to select and display significant results. Default `alpha=0.05`.
`scale_threshold` | threshold on the test scale (maximum interval length for the p-value adjustment) to be used in the adjusted p-value plot. Can be either a scalar (the same length for all features) or a vector (a length for each feature) or a list of vectors (a vector for each test). If `NULL`, the maximum possible interval length is used.
`nlevel` | number of desired color levels for the adjusted p-value heatmap.
`type` | type of plot to be drawn in addition to the adjusted p-value heatmap and plot. Possible types are: `"boxplot"` for the pointwise quantiles curves (default), `"curves"` for the (aligned) curves.
`N_regions` | number of regions to be randomly chosen (for each region dataset) in `"curves"` type plot. Default plots a maximum of 10 curves.
`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_features_subset` | vector with the identifiers of the features to be plotted.
`col` | vector of plotting colors for the different region datasets.
`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 feature measurement plot.
`...` | additional plot parameters.

### Value

No value returned. The function produces a graphical output.

### Author(s)

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

### References

A Pini and S Vantini (2017). Interval-Wise Testing for functional data. Journal of Nonparametric Statistics.

### See Also

`IWTomicsData` for `"IWTomicsData"` class, constructors, accessors and methods; `IWTomicsTest` function to perform the Interval-wise Testing; `plotSummary` to draw a summary plot of the test results.

### Examples

    data(regionsFeatures_center)

    ## One sample test for 'control' regions and feature 'ftr1'
    regionsFeatures_test=IWTomicsTest(regionsFeatures_center,
                                      id_region1='control',id_features_subset='ftr1')

    ## Plotting the results of the one sample test
    plotTest(regionsFeatures_test,col=5)

    ## Set the scale threshold to 25
    plotTest(regionsFeatures_test,col=5,scale_threshold=25)

    ## Plot curves instead of boxplots, do not report sample size in each position
    plotTest(regionsFeatures_test,col=5,type='curves',size=FALSE)

    ## Two sample test for 'elem1', 'elem2' and 'elem3' vs 'control' regions
    regionsFeatures_test=IWTomicsTest(regionsFeatures_center,
                                      id_region1=c('elem1','elem2','elem3'),
                                      id_region2=c('control','control','control'))

    ## Plotting the results of the two sample test
    plotTest(regionsFeatures_test)

    ## Set scale thresholds for the different features
    plotTest(regionsFeatures_test,scale_threshold=c(25,30))

    ## Plot only results regarding feature 'ftr2', setting scale thresholds for each test
    plotTest(regionsFeatures_test,id_features_subset='ftr2',
             scale_threshold=list(test1=10,test2=20,test3=30))

    ## Report also 0.05 and 0.95 quantiles in the boxplots
    plotTest(regionsFeatures_test,id_features_subset='ftr2',
             scale_threshold=list(test1=10,test2=20,test3=30),
             probs=c(0.05,0.25,0.5,0.75,0.9))

[Package IWTomics version 1.14.0 Index]