results_volcano {RQdeltaCT}

results_volcano

Description

This function creates volcano plot that illustrate the arrangement of genes based on fold change values and p values. Significant genes can be pointed out using specified p value and fold change thresholds, and highlighted on the plot by color and (optionally) isolated by thresholds lines.

Usage

results_volcano(
  data,
  mode,
  p.threshold = 0.05,
  FCh.threshold = 2,
  sel.Gene = "all",
  point.size = 4,
  point.shape = 19,
  alpha = 0.7,
  colors = c("#66c2a5", "#fc8d62"),
  add.thr.lines = TRUE,
  linewidth = 0.25,
  linetype = "dashed",
  x.axis.title = "log2(fold change)",
  y.axis.title = "-log10(p value)",
  axis.title.size = 11,
  axis.text.size = 10,
  legend.text.size = 11,
  legend.title = "Selected as significant?",
  legend.title.size = 11,
  legend.position = "top",
  plot.title = "",
  plot.title.size = 14,
  dpi = 600,
  width = 15,
  height = 15,
  save.to.tiff = FALSE,
  name.tiff = "results_volcano"
)

Arguments

data

Object returned from RQ_dCt() or RQ_ddCt() functions.

mode

Character: which p value should be used? One of the "t" (p values from Student's t test), "t.adj" (adjusted p values from Student's t test), "mw" (p values from Mann-Whitney U test),"mw.adj" (adjusted p values from Mann-Whitney U test), "depends" (if data in both compared groups were considered as derived from normal distribution (p value from Shapiro_Wilk test > 0.05) - p values from Student's t test will be used for significance assignment, otherwise p values from Mann-Whitney U test will be used), "depends.adj" (if data in both compared groups were considered as derived from normal distribution (p value from Shapiro_Wilk test > 0.05) - adjusted p values from Student's t test will be used for significance assignment, otherwise adjusted p values from Mann-Whitney U test will be used), and "user" that can be used the user intend to use another p values, e.g. obtained from other statistical test. In such situation, before run FCh_plot function, the user should prepare data frame object named "user" that contains two columns, the first of them with Gene names and the second with p values. The order of columns must be kept as described.

p.threshold

Numeric: threshold of p values for statistical significance.

FCh.threshold

Numeric: threshold of fold change values used for significance assignment of genes. If is set to 2 (default), genes with 2-fold changed expression (increased or decreased) between groups will be assigned as significant.

sel.Gene

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

point.size

Numeric: size of points. Default to 4.

point.shape

Integer: shape of points. Default to 19..

alpha

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

colors

Character vector length of two, containing colors for significant and no significant genes.

add.thr.lines

Logical, if TRUE (default), threshold lines will be added to the plot.

linewidth

Numeric: width of the added threshold lines. Default to 0.25.

linetype

Character: type of the added threshold lines. One of the "solid", "dashed" (default), "dotted", "dotdash", "longdash", "twodash", and "blank".

x.axis.title

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

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 10.

legend.text.size

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

legend.title

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

legend.title.size

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

legend.position

Position of the legend, can be one of "top" (default), "right", "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.

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.

save.to.tiff

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

name.tiff

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

Value

List containing object with barplot and data frame with results. Created plot is also displayed on graphic device.

Examples

library(ggsignif)
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")
data.dCtF <- filter_transformed_data(data.dCt, remove.Sample = c("Control11"))
results.dCt <- RQ_dCt(data.dCtF, "Disease", "Control")

RQ.volcano <- results_volcano(data = results.dCt,
                         mode = "depends",
                         p.threshold = 0.05,
                         FCh.threshold = 2)
head(RQ.volcano[[2]])