missPattern: Inspects Pattern of Missingness

In GonzalezIgnacio/missRows: Handling Missing Individuals in Multi-Omics Data Integration

Description

This function inspects and plots the structure of missing individuals in data tables.

Usage

missPattern(object, colStrata=NULL, colMissing="grey70", cexTitles=12,
            legTitle="Strata", missLab="miss", showPlot=TRUE)

## S3 method for class 'missPattern'
print(x, ...)

Arguments

object	an object of class MIDTList.
x	an object of class inheriting from missPattern
colStrata	a character vector of the same length than the number of strata, containing the color names to be used to annotate the individuals per stratum.
colMissing	the fill color for missing individuals.
cexTitles	a positive number. The amount by which table titles should be magnified.
legTitle	character. The legend title.
missLab	character. The label legend for missing individuals.
showPlot	logical. Whether the plot will be displayed. Default is TRUE.
...	not used currently.

Details

missPattern calculates the amount of missing/available individuals in each stratum per data table and plots a missingness map showing where missingness occurs. For plotting, tables are arranged in individuals (rows) x features (columns). Data tables are plotted separately on a same device showing the pattern of missingness. The individuals are colored according to their stratum whereas missing individuals (rows) are specific colored (see colMissing).

Value

A list with the following components:

nbMissing	a data.frame containing the amount of missing/available rows in each stratum per data table.
isMissing	a data.frame containing the indicator matrix for the missing rows.
ggp	an object of class ggplot.

Author(s)

Ignacio González

Examples

#-- load data and create MIDTList object
data(NCI60)
midt <- MIDTList(NCI60$mae)

#-- inspects pattern of missingness
patt <- missPattern(midt)
patt

GonzalezIgnacio/missRows documentation built on Jan. 16, 2020, 4:11 a.m.