plotSummarySignal: The function plotSummarySignal visualizes the...

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

The function plotSummarySignal visualizes the signalSummaryMatrix obtained from calcSummarySignal.

Description

The function plotSummarySignal visualizes the signalSummaryMatrix obtained from calcSummarySignal.

Usage

plotSummarySignal(
  signalSummaryList,
  plotType = "barPlot",
  metadata = NULL,
  colorColumn = NULL,
  filterGroupColumn = NULL,
  filterGroup = NULL
)

Arguments

signalSummaryList	Output list from calcSummarySignal function.
plotType	Options are: "jitter" - jitter plot with box plot on top, "boxPlot" - box plot without individual points and outliers, "barPlot" (default) - bar height represents the median signal value for a given cell type, "violinPlot" - violin plot with medians.
metadata	(optional) data.table used for grouping columns from 'signalMatrix' into categories, that are then plotted with different colors. Must contain variable 'colName' that contains all the condition column names from 'signaMatrix'.
colorColumn	(optional only if metadata provided) columns name from 'metadata' table that will be used as grouping variable for coloring.
filterGroupColumn	(optional only if metadata provided and 'filterGroup' specified) allows user to plot specified subgroups only. String specifying the column name in 'metadata' from which groups will be filtered (groups are specified in as 'filterGroups)
filterGroup	(optional only if 'metadata' and 'filterGroupColumn' provided) - string (or vector of strings) of groups from 'filterGroupColumn' to be plottted.

Value

A ggplot object.

Examples

signalSummaryList = calcSummarySignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)
metadata = cellTypeMetadata
plotSignal = plotSummarySignal(signalSummaryList)

plotSignalTissueColor = plotSummarySignal(signalSummaryList = signalSummaryList, 
plotType = "jitter", metadata = metadata, colorColumn = "tissueType")

plotSignalFiltered = plotSummarySignal(signalSummaryList = signalSummaryList,
plotType = "violinPlot", metadata = metadata, colorColumn = "tissueType", 
filterGroupColumn = "tissueType", filterGroup = c("skin", "blood"))

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.