doubledeepms__plot_heatmap_subset: doubledeepms__plot_heatmap_subset

In lehner-lab/doubledeepms: Analysis scripts to reproduce the figures and results from doubleDeepPCA manuscript

doubledeepms__plot_heatmap_subset

Description

ggplot subset and plot free energies heatmap.

Usage

doubledeepms__plot_heatmap_subset(input_file, output_file, mut_subset,
  pos_subset, order_mut_subset = T, width = 10, height = 4,
  units = "in", colour_clip = 4, cluster = "both", xlab = "",
  ylab = "", 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,
  input_matrix_point = NULL, text_size = 0.25, text_colour = "black",
  highlight_regions = NULL, x_breaks = ggplot2::waiver(),
  y_breaks = ggplot2::waiver(), show_legend = F, plot = T)

Arguments

input_file	data frame with heatmap values (required)
output_file	plot output file path
mut_subset	vector of aa mutations to show in the heat map y axis (required)
pos_subset	vector of domain positions to show in the heat map x axis (required)
order_mut_subset	whether the y axis should follow the order of aa of the mut_subset (True, False, default: True)
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
input_matrix_point	matrix of heatmap points (plotted instead of tiles)
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)
show_legend	whether to plot legend (True, False)
plot	whether to plot the heatmap (True, False)

Value

Nothing

lehner-lab/doubledeepms documentation built on July 21, 2023, 4:10 a.m.