timeSeriesGrid: Plot time series data

In umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

Description

Function for plotting time series or other meta data. Uses facet wrap to display user-provided categorical variables.

Usage

timeSeriesGrid(
  object,
  filter.name = "default",
  cut.off = 5,
  min.count = 0,
  min.vaf = 0,
  amplicons = NULL,
  samples = NULL,
  x_variable = NULL,
  y_variable = "Max Non-ref Allele Frequency",
  columns = "Sample Name",
  rows = "Name",
  color_by = "Name",
  fdr = 0.05,
  use.caller = TRUE,
  bed_positions = NULL
)

Arguments

object	A consensus data table
filter.name	"default"
cut.off	5
min.count	0
min.vaf	0
amplicons	NULL
samples	NULL
x_variable	NULL
y_variable	"Max Non-ref Allele Frequency"
columns	"Sample Name"
rows	"Name"
color_by	"Name"
fdr	0.05
use.caller	TRUE
bed_positions	NULL

Value

A ggplot object.

Examples

library(umiAnalyzer)

main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main)
simsen <- filterUmiObject(simsen)

metaData <- system.file("extdata", "metadata.txt", package = "umiAnalyzer")
simsen <- importDesign(object = simsen,file = metaData)

bed_dir <- system.file("extdata", "simple.bed", package = "umiAnalyzer")
bed <- importBedFile(path = bed_dir)

time_plot <- timeSeriesGrid(simsen, x_variable = "time", bed_positions = bed)

umiAnalyzer documentation built on Nov. 25, 2021, 9:07 a.m.