image_with_text: Plot a heatmap

Description Usage Arguments Value

View source: R/image_with_text.R

Description

Plot a heatmap

Usage

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image_with_text(
  mat,
  xlab = "",
  ylab = "",
  main = NULL,
  main_shift = 0.12,
  col_names = colnames(mat),
  row_names = rownames(mat),
  row_text_adj = 1,
  row_text_shift = 0,
  row_text_rotation = 0,
  col_text_rotation = 90,
  col_text_adj = 1,
  col_text_shift = 0,
  show_text = TRUE,
  cex = 0.5,
  col_text_cex = 1,
  row_text_cex = 1,
  main_cex = 1,
  split_at_vals = FALSE,
  split_points = 0,
  col_scale = "gray",
  color_spread = 50,
  light_dark = "f",
  class_mat = NULL,
  grad_dir = c("high", "low", "middle", "ends"),
  color_fun = c("linear", "exponential"),
  exp_steepness = 1,
  global_color_scale = FALSE,
  global_min = NULL,
  global_max = NULL,
  sig_digs = 3,
  use_pheatmap_colors = FALSE,
  na_col = "lightgray",
  gridlines = FALSE
)

Arguments

mat

A numeric matrix to plot as a heat map

xlab

A string label for the x axis

ylab

A string label for the y axis

main

A title for the plot

main_shift

A numeric value to shift the title along the y axis.

col_names

A vector of strings indicating names for the columns of the matrix. Defaults to existing column names.

row_names

A vector of strings indicating names for the rows of the matrix. Defaults to existing row names.

row_text_adj

adjustment value for row text indicating the centering. See text.

row_text_shift

numeric value for shifting the row labels toward or away from the matrix.

row_text_rotation

Rotation value in degrees for the row labels

col_text_rotation

Rotation value in degrees for the column labels

col_text_adj

adjustment value for column text indicating the centering. See text.

col_text_shift

numeric value for shifting the column labels toward or away from the matrix.

show_text

Whether to write the numerical value of each cell in the plot.

cex

The size of the text when show_text is TRUE

col_text_cex

The size of the column labels

row_text_cex

The size of the row labels

main_cex

The size of the title of the plot

split_at_vals

Whether to split the values into different color classes

split_points

If split_at_vals is TRUE, split_points determines the boundaries of the classes. For example, if split_points is 0, negative and positive numbers will be assigned to different color classes.

col_scale

One of c("green", "purple", "orange", "blue", "brown", "gray") to indicate the color scale to be used. Defaults to gray.

color_spread

A numerical value used as input to get_color2 indicating the numeric distance between colors in a ramp. Smaller values produce a smaller difference between adjacent colors in the ramp.

light_dark

One of "l", "d", or "f" indicating whether the colors used should be light ("l"), dark ("d"), or from across the full spectrum ("f").

class_mat

An optional numeric matrix defining the color classes of each cell in the matrix. If omitted this is calculated by the function.

grad_dir

A string specifying how the color gradient should be applied. If "high" higher values are given darker colors. If "low", lower values are given darker colors. If "middle" values in the middle of the spectrum are given darker colors, and if "end" values at the ends of the spectrum are given darker colors.

color_fun

Either "linear" or "exponential" indicating how the colors should transition from light to dark across values.

exp_steepness

If color_fun is "exponential," exp_steepness indicates how quickly the colors should transition from light to dark.

global_color_scale

Whether to impose a global minimum and maximum to the colors, or to use the values themselves to determine the top and bottom of the color scale.

global_min

If global_color_scale is TRUE, the minimum value that should be assigned a color.

global_max

If global_color_scale is TRUE, the maximum value that should be assigned a color.

sig_digs

The number of significant figures to use from the input matrix. Helpful primarily when show_text is TRUE.

use_pheatmap_colors

If TRUE, all other color parameters are ignored, and colors like those used in the R package pheatmap are used instead.

na_col

The color to use for missing values.

gridlines

Whether to plot gridlines on the matrix.

Value

None


cape documentation built on Feb. 10, 2021, 5:06 p.m.