control_boxplot_sample {RQdeltaCT}

control_boxplot_sample

Description

Boxplot that illustrate distribution of data in each sample. This function is helpful to identify outlier samples.

Usage

control_boxplot_sample(
  data,
  sel.Sample = "all",
  pairwise.FCh = FALSE,
  coef = 1.5,
  colors = c("#66c2a5", "#fc8d62"),
  x.axis.title = "Sample",
  y.axis.title = "value",
  axis.title.size = 11,
  axis.text.size = 12,
  legend.title = "Group",
  legend.title.size = 11,
  legend.text.size = 11,
  legend.position = "right",
  plot.title = "",
  plot.title.size = 14,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "control_boxplot_samples"
)

Arguments

data

Object returned from make_Ct_ready() or delta_Ct() functions. Also, a data frame with fold change values returned from RQ_dCt() and RQ_ddCt() functions run in a pairwise mode can be used.

sel.Sample

Character vector with names of samples to include, or "all" (default) to use all samples.

pairwise.FCh

Logical: If fold change values returned from RQ_dCt() and RQ_ddCt() functions in a pairwise approach are used as data, this parameter should be set to TRUE, otherwise to FALSE (default).

coef

Numeric: how many times of interquartile range should be used to determine range point for whiskers. Default to 1.5.

colors

Character vector containing colors for compared groups. Numbers of colors must be equal to number of groups. Default to c("#66c2a5", "#fc8d62"). If pairwise.FCh parameter is set to TRUE, one color is required (data contain no groups).

x.axis.title

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

y.axis.title

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

axis.title.size

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

axis.text.size

Integer: font size of axis text. Default to 12.

legend.title

Character: title of legend. Default to "Group".

legend.title.size

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

legend.text.size

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

legend.position

Position of the legend, can be "top", "right" (default), "bottom", "left", or "none" (no legend). See description for legend.position 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 "control_boxplot_samples".

Value

Object with a boxplot illustrating distribution of data in each sample. Created plot is also displayed on the graphic device.

Examples

library(tidyverse)
data(data.Ct)
data.CtF <- filter_Ct(data.Ct,
                      remove.Gene = c("Gene2","Gene5","Gene6","Gene9","Gene11"),
                      remove.Sample = c("Control08","Control16","Control22"))
data.CtF.ready <- make_Ct_ready(data.CtF, imput.by.mean.within.groups = TRUE)
data.dCt <- delta_Ct(data.CtF.ready, ref = "Gene8")
control.boxplot.sample <- control_boxplot_sample(data.dCt)