generateProfilePlot: Import ChIPprofile object to profileplyr

In RockefellerUniversity/profileplyr: Visualization and annotation of read signal over genomic ranges with profileplyr

Import ChIPprofile object to profileplyr

Description

Function to convert soGGi ChIPprofile objects to profileplyr object .

Usage

generateProfilePlot(
  object,
  sampleNames = rownames(sampleData(object)),
  colorGroup = params(object)$rowGroupsInUse,
  colorlist = NULL,
  facet_nrow = 1,
  facet_ncol = NULL,
  facet_scales = "fixed"
)

Arguments

object	A profileplyr object
sampleNames	The names used to label the samples in the profileplyr object. By default, the names stored in rownames(sampleData(object)) are used.
colorGroup	The name of the column in mcols(object) that will be used for color grouping in the plot. By default the column name in params(object)$rowGroupsInUse is used. If this column is not a factor variable, then it will be converted into one.
colorlist	A vector containing the colors to be used. The positions in the vector will be matched with the levels of the factor variable chosen in the 'colorGroup' argument.
facet_nrow	The number of rows when making the plot panels. This argument is passed to 'nrow' of the ggplot2 function facet_wrap.
facet_ncol	The number of columns when making the plot panels. This argument is passed to 'ncol' of the ggplot2 function facet_wrap.
facet_scales	Whether the scales of all plot panels should be fixed ("fixed", default), free ("free"), or free in one dimension ("free_x" or "free_y"). This argument is passed to 'scales' of the ggplot2 function facet_wrap.

Value

A profileplyr object

Examples

example <- system.file("extdata", "example_deepTools_MAT", package = "profileplyr") 
object <- import_deepToolsMat(example)

generateProfilePlot(object)

RockefellerUniversity/profileplyr documentation built on Jan. 28, 2023, 10:09 a.m.