vizu.mat {mdpeer}

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

Description

Matrix data visualization in a form of a heatmap, with the use of ggplot2 library. Minimum user input (a matrix object) is needed to produce decent visualization output. Automatic plot adjustments are implemented and used as defaults, including selecting legend color palette and legend scale limits. Further plot adjustments are available, including adding a title, font size change, axis label clearing and others.

Usage

vizu.mat(matrix.object, title = "", base_size = 12, adjust.limits = TRUE,
  adjust.colors = TRUE, fill.scale.limits = NULL, colors.palette = 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,
  axis.text.x.breaks.idx = NULL, axis.text.y.breaks.idx = NULL)

Arguments

matrix.object

matrix

title

plot title

base_size

base font size

adjust.limits

logical whether or not adjust legend scale limits automatically:

• legend scale starts / ends with 0 for matrix with non-negative / non-positive values only,

• legend scale is symmetric for matrix with both negative and positive values

adjust.colors

logical whether or not adjust legend color automatically:

• legend color palette white-red for a data matrix with non-negative values only,

• legend color palette blue-white for a data matrix with non-positive values only,

• legend color palette blue-white-red for a data matrix with both positive and negative values

fill.scale.limits

2-element vector defining legend scale limits

colors.palette

legend color color palette

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

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 <- matrix(rnorm(30*30), nrow = 30, ncol = 30)
vizu.mat(mat)
vizu.mat(mat, fill.scale.limits = c(-3,3))
vizu.mat(mat, fill.scale.limits = c(-10,10))
vizu.mat(mat, fill.scale.limits = c(-10,10), 
         uniform.labes = TRUE, 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(mat, fill.scale.limits = c(-10,10), 
         clear.labels = FALSE, 
         rotate.x.labels = TRUE)
mat.positive <- abs(mat)
vizu.mat(mat.positive, 
         title = "positive values only -> legend limits and colors automatically adjusted",
         clear.labels = FALSE, 
         rotate.x.labels = TRUE)