control_Ct_barplot_gene {RQdeltaCT}

control_Ct_barplot_gene

Description

Gene-wide quality control of raw Ct values across groups by illustrating numbers of Ct values labelled as reliable or not by using reliability criteria (see function parameters).

Usage

control_Ct_barplot_gene(
  data,
  flag.Ct = "Undetermined",
  maxCt = 35,
  flag = "Undetermined",
  colors = c("#66c2a5", "#fc8d62"),
  x.axis.title = "",
  y.axis.title = "Number",
  axis.title.size = 11,
  axis.text.size = 10,
  legend.title = "Reliable Ct value?",
  legend.title.size = 11,
  legend.text.size = 11,
  legend.position = "top",
  plot.title = "",
  plot.title.size = 14,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "Ct_control_barplot_for_genes"
)

Arguments

data

Object returned from read_Ct_long() or read_Ct_wide() function, or data frame containing column named "Sample" with sample names, column named "Gene" with gene names, column named "Ct" with raw Ct values, column named "Group" with group names. Optionally, data frame can contain column named "Flag" with flag information (e.g. "Undetermined" and "OK"), which will be used for reliability assessment.

flag.Ct

Character of a flag used for undetermined Ct values. Default to "Undetermined".

maxCt

Numeric, a maximum of Ct value allowed. Default to 35.

flag

Character of a flag used in the Flag column for values which are unreliable. Default to "Undetermined".

colors

Character vector length of two, containing colors for Ct values which are labelled as reliable (first element of vector) or not (second element of vector).

x.axis.title

Character: title of x axis. Default to "".

y.axis.title

Character: title of y axis. Default to "Number".

axis.title.size

Integer: font size of axis titles. Default to 11.

axis.text.size

Integer: font size of axis text. Default to 10.

legend.title

Character: title of legend. Default to "Reliable Ct value?".

legend.title.size

Integer: font size of legend title. Default to 12.

legend.text.size

Integer: font size of legend text. Default to 11.

legend.position

Position of the legend, can be "top" (default), "right", "bottom", "left", or "none" (no legend). See description for legend.position parameter in ggplot2::theme() function.

plot.title

Character: title of plot. Default to "".

plot.title.size

Integer: font size of plot title. Default to 14.

save.to.tiff

Logical: if TRUE, plot will be saved as .tiff file. Default to FALSE.

dpi

Integer: resolution of saved .tiff file. Default to 600.

width

Numeric: width (in cm) of saved .tiff file. Default to 15.

height

Numeric: height (in cm) of saved .tiff file. Default to 15.

name.tiff

Character: name of saved .tiff file, without ".tiff" name of extension. Default to "Ct_control_barplot_for_genes".

Details

This function does not perform data filtering, but only counts Ct values labelled as reliable or not and presents them graphically. Could be useful to identify genes with low number of reliable Ct values.

Value

List containing plot and table with counts of reliable and non reliable Ct values in genes. Additional information about returned table is also printed to help the user to properly interpret returned table. Plot is also displayed on the graphic device.

Examples

library(tidyverse)
data(data.Ct)
gene.Ct.control <- control_Ct_barplot_gene(data.Ct)
gene.Ct.control[[2]]