control_boxplot_gene {RQdeltaCT}

control_boxplot_gene

Description

This function creates boxplot that illustrate distribution of data in each gene.

Usage

control_boxplot_gene(
  data,
  sel.Gene = "all",
  pairwise.FCh = FALSE,
  coef = 1.5,
  by.group = TRUE,
  colors = c("#66c2a5", "#fc8d62"),
  axis.title.size = 11,
  axis.text.size = 12,
  x.axis.title = "Gene",
  y.axis.title = "value",
  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_genes"
)

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.Gene

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

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.

by.group

Logical: if TRUE, distributions will be drawn by compared groups of samples.

colors

Character vector containing colors for groups, length of one (when by.group = FALSE) or equal to the number of groups (when by.group = TRUE).

axis.title.size

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

axis.text.size

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

x.axis.title

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

y.axis.title

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

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_genes".

Value

Object with boxplot illustrating distribution of data for each gene. 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.gene <- control_boxplot_gene(data.dCt)