tardbpdms__tile_heatmap_wrapper: tardbpdms__tile_heatmap_wrapper

In lehner-lab/tardbpdms: Analysis scripts for processing TDP-43 DMS data from Bolognesi et al. 2019.

Description

ggplot tile heatmap wrapper.

Usage

tardbpdms__tile_heatmap_wrapper(input_matrix, output_file, width = 10,
  height = 4, units = "in", colour_clip = 4, cluster = "both",
  xlab = "x", ylab = "y", xtick_labels = NULL, ytick_labels = NULL,
  colour_type = "continuous", colour_low = "blue",
  colour_high = "red", colour_mid = "white", colour_midpoint = 0,
  colour_limits = NULL, mono = F, na_colour = "grey50",
  xaxis_angle = 330, xaxis_hjust = 0, xaxis_vjust = NULL,
  xaxis_size = 5, omit_xtext = F, omit_xticks = F,
  yaxis_angle = NULL, yaxis_hjust = NULL, yaxis_vjust = NULL,
  yaxis_size = NULL, omit_ytext = F, omit_yticks = F,
  plot_title = "", input_matrix_text = NULL, text_size = 0.25,
  text_colour = "black", highlight_regions = NULL,
  x_breaks = ggplot2::waiver(), y_breaks = ggplot2::waiver(),
  plot = T)

Arguments

input_matrix	matrix of heatmap values (required)
output_file	plot output file path
width	plot width in "units"
height	plot height in "units"
units	plot size units ("in", "cm", or "mm")
colour_clip	maximum absolute value of colour scale
cluster	heirarchically cluster ("none", "row", "column", "none")
xlab	x-axis label
ylab	y-axis label
xtick_labels	display labels for x ticks
ytick_labels	display labels for y ticks
colour_type	colour scale type ("continuous", "categorical")
colour_low	colour scale lower limit colour – passed to scale_colour_gradient2
colour_high	colour scale upper limit colour – passed to scale_colour_gradient2
colour_mid	colour scale zero colour – passed to scale_colour_gradient2
colour_midpoint	midpoint for colour scale – passed to scale_colour_gradient2
colour_limits	upper and lower value limits of colour scale – passed to scale_colour_gradient2
mono	use monotype font (True, False)
na_colour	colour to use for NA values
xaxis_angle	rotation angle for x tick labels – passed to element_text
xaxis_hjust	horizontal justification of x tick labels (in [0, 1]) – passed to element_text
xaxis_vjust	vertical justification of x tick labels (in [0, 1]) – passed to element_text
xaxis_size	text size of x tick labels (in pts) – passed to element_text
omit_xtext	omit x tick labels (True, False)
omit_xticks	omit x ticks (True, False)
yaxis_angle	rotation angle for y tick labels – passed to element_text
yaxis_hjust	horizontal justification of y tick labels (in [0, 1]) – passed to element_text
yaxis_vjust	vertical justification of y tick labels (in [0, 1]) – passed to element_text
yaxis_size	text size of y tick labels (in pts) – passed to element_text
omit_ytext	omit y tick labels (True, False)
omit_yticks	omit y ticks (True, False)
plot_title	main title for plot
input_matrix_text	matrix of heatmap text
text_size	size of heatmap text
text_colour	colour of heatmap text
highlight_regions	list of highlighted regions of form: list("red" = list("region1" = c(_min_, _max_), "region2" = c(_min_, _max_), ...), "blue" = list("region3" = c(_min_, _max_), ...), ...)
x_breaks	x-axis breaks (for displaing xtick_labels)
y_breaks	y-axis breaks (for displaing ytick_labels)
plot	whether to plot the heatmap (True, False)

Value

Nothing

lehner-lab/tardbpdms documentation built on July 19, 2019, 7:24 p.m.