umiAnalyzer (version 1.0.0)

timeSeriesGrid: Plot time series data

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

# NOT RUN {
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)

# }