QcConfig: QcConfig

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

QcConfig

Description

QcConfig

QcConfig

QcColorMapping

QcColorMapping for QcConfig

QcScaleColor for QcConfig

QcScaleFill

QcScaleFill for QcConfig

QcConfig.save_config

Usage

QcConfig.files(
  file_paths,
  groups = NULL,
  group_names = NULL,
  group_colors = NULL
)

QcColorMapping(object)

## S4 method for signature 'QcConfig'
QcColorMapping(object)

## S4 method for signature 'QcConfig'
QcScaleColor(object)

QcScaleFill(object)

## S4 method for signature 'QcConfig'
QcScaleFill(object)

## S4 method for signature 'QcConfig'
show(object)

QcConfig.save_config(object, file)

Arguments

file_paths	character paths to files
groups	numeric vector of group assignments. 1 is first item in group_names, 2 is second, etc. Default is seq_along(file_path)
group_names	vector of group names to assign from according to groups
group_colors	vector of colors to use per group
object	QcConfig object to save to text file.
QcConfig

Value

A QcConfig object

a named vector of colors

a ggplot2 scale_fill_manual

invisibly returns path to saved config file.

Slots

file_paths

character.

groups

numeric.

group_names

character.

group_colors

character.

Examples

QcConfig.files(c("A", "B"))
QcColorMapping(QcConfig(c("A", "B")))
my_df = data.frame(group = c("A", "B"))
my_df$x = 1:2
my_df$y = 1
library(ggplot2)
ggplot(my_df, aes(x = x, y = y, color = group)) +
  geom_point(size = 20) +
  expand_limits(x = c(0, 3)) +
  QcScaleColor(QcConfig(my_df$group))
my_df = data.frame(group = c("A", "B"))
my_df$x = 1:2
my_df$y = 1
library(ggplot2)
ggplot(my_df, aes(x = x, y = y, fill = group)) +
  geom_point(size = 20, pch = 22) +
  expand_limits(x = c(0, 3)) +
  QcScaleFill(QcConfig(my_df$group))
cfg_file = system.file("extdata/ssvQC_peak_config.csv", package = "ssvQC")
qc_features = QcConfigFeatures.parse(cfg_file)
f = tempfile()
QcConfig.save_config(qc_features, f)

FrietzeLabUVM/ssvQC documentation built on March 25, 2024, 12:24 a.m.