single_pair_gene {RQdeltaCT}

single_pair_gene

Description

This function generates scatter plot with linear regression line for two specified genes.

Usage

single_pair_gene(
  data,
  x,
  y,
  by.group = TRUE,
  point.size = 4,
  point.shape = 19,
  point.alpha = 0.7,
  colors = c("#66c2a5", "#fc8d62"),
  axis.title.size = 11,
  axis.text.size = 10,
  legend.title = "Group",
  legend.title.size = 11,
  legend.text.size = 11,
  legend.position = "right",
  plot.title = "",
  plot.title.size = 14,
  labels = TRUE,
  label = c("eq", "R2", "p"),
  label.position.x = c(1, 1),
  label.position.y = c(1, 0.95),
  small.p = FALSE,
  small.r = FALSE,
  p.digits = 3,
  rr.digits = 2,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "_single_pair_plot"
)

Arguments

data

Object returned from make_Ct_ready() or delta_Ct() functions.

x, y

Characters: names of genes to use.

by.group

Logical: if TRUE (default), relationships will be shown separately for compared groups.

point.size

Numeric: size of points. Default to 4.

point.shape

Integer: shape of points. Default to 19.

point.alpha

Numeric: transparency of points, a value between 0 and 1. Default to 0.7.

colors

Character vector containing colors for compared groups. The number of colors must be equal to the number of groups. Default to c("#66c2a5", "#fc8d62").

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 "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 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.

labels

Logical: if TRUE (default), a regression statistics will be added to the plot using ggpimsc::stat_poly_eq() function.

label

Character: specifies regression statistics to add, names specified by ggpimsc::stat_poly_eq() function must be used. Default to c("eq", "R2", "p") for regression equation, coefficient of determination and p value, respectively.

label.position.x, label.position.y

Numeric: coordinates for position of regression statistics. If by.group = TRUE, a vector length of groups number can be provided to avoid overlapping. See description of label.x and label.y parameters from ggpimsc::stat_poly_eq() function.

small.p, small.r

Logical, if TRUE, p character in p value label and r character in coefficient of determination label will be lowercase. Default to FALSE.

rr.digits, p.digits

Integer: number of digits after the decimal point in coefficient of determination and p value in labels. Default to 2 for rr.digits and 3 for p.digits.

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 "Gene1_Gene2_single_pair_plot".

Value

Object with plot. Created plot is also displayed on the graphic device.

Examples

library(tidyverse)
library(ggpmisc)
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")
single_pair_gene(data.dCt, "Gene16", "Gene17")