plotlinc-methods: Plot Objects Of The 'LINC' class

In ManuelGoepferich/LINC_before_DEVEL: annotation of noncoding RNAs and coexpressed genes

Description

plotlinc is the generic function that creates plots based on objects of the LINC class.

Usage

plotlinc(input,
         showCor,
         returnDat = FALSE)

Arguments

input	usually a LINCmatrix, LINCcluster, LINCbio or LINCsingle object
showCor	a vector of gene names; length 2 up to 6 elements; the first entry is the subject (see example)
returnDat	whether to return the data used to create the plot TRUE or not FALSE

Details

A plot will be created based on the information found in the slots: history and linCenvir of a LINCmatrix, LINCcluster, LINCbio or LINCsingle object. Using the argument showCor = ... will output scatterplots for one query, the first entry in ..., and up to five subjects (see example). This can be used to manually check the correlation of genes. Individual or modified plots can be generated by returning the plotting data with returnDat Unexpected extreme values may corrupt plots.

Value

an object of the class 'gtable' containing multiple 'grobs' or a 'list' if returnDat = TRUE

Methods

signature(input = "LINCbio", showCor = "character")

(see details)

signature(input = "LINCbio", showCor = "missing")

(see details)

signature(input = "LINCcluster", showCor = "character")

(see details)

signature(input = "LINCcluster", showCor = "missing")

(see details)

signature(input = "LINCmatrix", showCor = "character")

(see details)

signature(input = "LINCmatrix", showCor = "missing")

(see details)

signature(input = "LINCsingle", showCor = "character")

(see details)

signature(input = "LINCsingle", showCor = "missing")

(see details)

Compatibility

plotlinc(LINCmatrix, ...), plotlinc(LINCcluster, ...), plotlinc(LINCbio, ...),plotlinc(LINCsingle, ...), ...

Author(s)

Manuel Goepferich

See Also

querycluster ; feature

Examples

data(BRAIN_EXPR)
plotlinc(crbl_matrix)
plotlinc(crbl_cluster)

# show correlations and expression; "647979" as query plus 4 subjects
plotlinc(crbl_cluster, showCor = c("647979", "6726", "3337", "3304" ,"3320"))

ManuelGoepferich/LINC_before_DEVEL documentation built on May 7, 2019, 2:46 p.m.