vizu.mat.factor: Visualize matrix data in a form of a heatmap, with...

In mdpeer: Graph-Constrained Regression with Enhanced Regularization Parameters Selection

Description

Matrix data visualization in a form of a heatmap, with the use of ggplot2 library. Numerical values are represented as categorical. Minimum user input (a matrix object) is needed to produce decent visualization output. Further plot adjustments are available, including tile color change, adding a title, font size change, axis label clearing and others.

Usage

vizu.mat.factor(matrix.object, title = "", base_size = 12,
  scale_fill_manual.values = NULL, geom_tile.colour = "grey90",
  clear.labels = TRUE, clear.x.label = FALSE, clear.y.label = FALSE,
  uniform.labes = FALSE, rotate.x.labels = FALSE, x.lab = "",
  y.lab = "", axis.text.x.size = base_size - 2,
  axis.text.y.size = base_size - 2, axis.title.x.size = base_size - 2,
  axis.title.y.size = base_size - 2, legend.text.size = base_size - 2,
  legend.title.size = base_size - 2, legend.title = "value",
  text.font.family = "Helvetica", remove.legend = FALSE,
  factor.levels = NULL, axis.text.x.breaks.idx = NULL,
  axis.text.y.breaks.idx = NULL)

Arguments

matrix.object	matrix
title	plot title
base_size	base font size
scale_fill_manual.values	vector of legend colors for categorical values
geom_tile.colour	tiles color value
clear.labels	logical whether or not clear both x- and y-axis labels
clear.x.label	logical whether or not clear x-axis labels
clear.y.label	logical whether or not clear y-axis labels
uniform.labes	logical whether or not define generic short column and rows labeling: 'c1','c2',...,'cp' for columns, 'r1','r2',...,'rp' for rows; might be especially useful if the matrix some long colnames and rownames already assigned
rotate.x.labels	logical whether or not rotate x-axis labels by 90 degrees
x.lab	x-axis label
y.lab	y-axis label
axis.text.x.size	font size of x-axis text
axis.text.y.size	font size of y-axis text
axis.title.x.size	font size of x-axis label
axis.title.y.size	font size of y-axis label
legend.text.size	font size of legend text
legend.title.size	font size of legend title
legend.title	legend title
text.font.family	font family
remove.legend	logical whether or not remove legend
factor.levels	vector of values defining levels of factors (might be used to redefine order of variables in the legend)
axis.text.x.breaks.idx	indices of x-axis elements whose thicks are kept and whose numerical labels are kept
axis.text.y.breaks.idx	indices of y-axis elements whose thicks are kept and whose numerical labels are kept

Value

ggplot2 object

Examples

mat <- diag(30)
vizu.mat.factor(mat)
vizu.mat.factor(mat, 
                title = "some title",
                scale_fill_manual.values = c("white","red"),
                axis.text.x.breaks.idx = seq(1,30,5),
                axis.text.y.breaks.idx = seq(1,30,5))
vizu.mat.factor(mat, 
                title = "some title: large font, legend: small font",
                base_size = 20, 
                legend.text.size  = 10, 
                legend.title.size = 10)
vizu.mat.factor(mat, 
                scale_fill_manual.values = c("white","red"),
                clear.labels = FALSE) 
colnames(mat) <- paste0("col", 1:30, sample(LETTERS, 30, replace = TRUE))
rownames(mat) <- paste0("row", 1:30, sample(LETTERS, 30, replace = TRUE))
vizu.mat.factor(mat, 
                clear.labels = FALSE,
                rotate.x.labels = TRUE) 

mdpeer documentation built on May 2, 2019, 3:36 p.m.