vizu.mat.factor {mdpeer}

Visualize matrix data in a form of a heatmap, with categorical values legend

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)