control_pca_sample {RQdeltaCT}

control_pca_sample

Description

This function performs principal component analysis (PCA) for samples and generate plot that illustrate spatial arrangement of samples based on the two first components. This plot is useful to identify outlier samples. PCA analysis can not deal with missing values, thus all samples with at least one missing value are removed from data before analysis.

Usage

control_pca_sample(
  data,
  sel.Gene = "all",
  pairwise.FCh = FALSE,
  point.size = 4,
  point.shape = 19,
  alpha = 0.7,
  colors = c("#66c2a5", "#fc8d62"),
  label.size = 3,
  hjust = 0.5,
  vjust = -1,
  axis.title.size = 11,
  axis.text.size = 10,
  legend.text.size = 11,
  legend.title = "Group",
  legend.title.size = 11,
  legend.position = "right",
  plot.title = "",
  plot.title.size = 14,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "control_pca_samples"
)

Arguments

data

Object returned from make_Ct_ready() or delta_Ct() functions. Also, table with fold change values returned from RQ_dCt() and RQ_ddCt() functions can be used, but in such situation a pairwise.FCh parameter must be set to TRUE.

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).

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

label.size

Numeric: size of points labels (names of samples). Default to 3.

hjust

Numeric: horizontal position of points labels. Default to 0.

vjust

Numeric: vertical position of points labels. Default to -1.

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 "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.

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_pca_samples".

Value

Object with plot. The 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_pca_sample(data.dCt)