plotlinc-methods: Plot Objects Of The 'LINC' class
In LINC: co-expression of lincRNAs and protein-coding genes

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

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

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plotlinc(input,
         showCor,
         returnDat = FALSE)

`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`

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.

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

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)

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

Manuel Goepferich

querycluster ; feature

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"))