results_heatmap {RQdeltaCT}

results_heatmap

Description

This function creatse heatmap with hierarchical clustering.

Usage

results_heatmap(
  data,
  sel.Gene = "all",
  dist.row = "euclidean",
  dist.col = "euclidean",
  clust.method = "average",
  col.groups,
  colors = c("navy", "#313695", "#4575B4", "#74ADD1", "#ABD9E9", "#E0F3F8", "#FFFFBF",
    "#FEE090", "#FDAE61", "#F46D43", "#D73027", "#C32B23", "#A50026", "#8B0000",
    "#7E0202", "#000000"),
  show.colnames = TRUE,
  show.rownames = TRUE,
  border.color = NA,
  fontsize = 10,
  fontsize.col = 10,
  fontsize.row = 10,
  angle.col = 0,
  cellwidth = NA,
  cellheight = NA,
  save.to.tiff = FALSE,
  dpi = 600,
  width = 15,
  height = 15,
  name.tiff = "heatmap_results"
)

Arguments

data

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

sel.Gene

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

dist.row, dist.col

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

clust.method

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".

col.groups

A named list with colors for groups annotation (see example).

colors

Vector with colors used to fill created heatmap.

show.colnames, show.rownames

Logical: of TRUE, names of columns (sample names) and rows (gene names) will be shown. Both default to TRUE.

border.color

Character: color of cell borders on heatmap. If set to NA (default) no border will be drawn.

fontsize

Numeric: global fontsize of heatmap. Default to 10.

fontsize.col, fontsize.row

Numeric: fontsize of colnames and rownames. Default to 10.

angle.col

Integer: angle of the column labels, one of the 0, 45, 90, 270, and 315.

cellwidth, cellheight

Numeric: width and height of individual cell. Both default to NA. These parameters are useful in situations where margins are too small and the plot is cropped (column names and annotation legend are sometimes partially hidden). Specification of this parameter allows to adjust size of the plot and solve this problem.

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 "heatmap_results".

Value

Heatmap with hierarchical clustering, displayed on the graphic device (if save.to.tiff = FALSE) or saved to .tiff file (if save.to.tiff = TRUE).

Examples

library(tidyverse)
library(pheatmap)
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")
# Remember to firstly create named list with colors for groups annotation:
colors.for.groups = list("Group" = c("Disease"="firebrick1","Control"="green3"))
# Vector of colors to fill the heatmap can be also specified to fit the user needings:
colors <- c("navy","navy","#313695","#4575B4","#74ADD1","#ABD9E9",
            "#E0F3F8","#FFFFBF","#FEE090","#FDAE61","#F46D43",
            "#D73027","#C32B23","#A50026","#8B0000",
            "#7E0202","#000000")
results_heatmap(data.dCt,
                sel.Gene = "all",
                col.groups = colors.for.groups,
                colors = colors,
                show.colnames = FALSE,
                show.rownames = TRUE,
                fontsize = 11,
                fontsize.row = 11)