control_cluster_sample {RQdeltaCT}

control_cluster_sample

Description

This function performs hierarchical clustering of samples based on the data, useful to identify outlier samples.

Usage

control_cluster_sample(
  data,
  sel.Gene = "all",
  method.dist = "euclidean",
  method.clust = "average",
  pairwise.FCh = FALSE,
  x.axis.title = "Samples",
  y.axis.title = "Height",
  label.size = 0.8,
  plot.title = "",
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "control_clust_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.

method.dist

Character: name of method used for calculation of distances, derived from stats::dist() function, must be one of "euclidean" (default) , "maximum", "manhattan", "canberra", "binary" or "minkowski".

method.clust

Character: name of used method for agglomeration, derived from stats::hclust() function, must be one of "ward.D", "ward.D2", "single", "complete", "average" (default), "mcquitty", "median" or "centroid".

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).

x.axis.title

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

y.axis.title

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

label.size

Numeric: size of text labels. Default to 0.8.

plot.title

Character: title of plot. Default to "".

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_clust_samples".

Value

Plot with hierarchical clustering of samples, 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_cluster_sample(data.dCt)