plot_alignment: Plot alignment of variables
In linnykos/multiomicCCA: Tilted CCA

plot_alignment

R Documentation

Plot alignment of variables

Description

Plot alignment of variables

Usage

plot_alignment(
  rsquare_vec,
  logpval_vec,
  bool_hide_points = F,
  bool_mark_ymedian = F,
  bool_polygon_mean = T,
  bool_truncate_xaxis = T,
  bool_white_bg = T,
  bty = "n",
  cex_axis = 1,
  cex_gene_highlight_inner = 3,
  cex_gene_highlight_outer = 4,
  cex_lab = 1,
  cex_points = 2,
  col_points = grDevices::rgb(0.5, 0.5, 0.5, 0.1),
  col_gene_highlight = 2,
  col_gene_highlight_border = "white",
  col_grid = "gray",
  density = 20,
  gene_names = NULL,
  lty_grid_major = 2,
  lty_grid_minor = 3,
  lty_polygon = 2,
  lwd_axis = 1,
  lwd_axis_ticks = 1,
  lwd_grid_major = 1,
  lwd_grid_minor = 0.5,
  lwd_polygon = 1,
  lwd_polygon_bold = 2,
  mark_median_xthres = 1,
  pch = 16,
  xaxt_num_ticks = 10,
  xaxt_grid_spacing = 2,
  xlab = "Separability (Median -Log10(p-value))",
  xlim = NULL,
  yaxt_by = 0.1,
  yaxt_num_ticks = 2,
  ylab = "Alignment with common space (R^2)",
  ylim = NULL,
  verbose = T,
  ...
)

Arguments

`rsquare_vec`	output of `tiltedCCA::postprocess_modality_alignment`
`logpval_vec`	output of `tiltedCCA::postprocess_depvalue`
`bool_hide_points`	boolean (graphical parameter)
`bool_mark_ymedian`	boolean (graphical parameter)
`bool_polygon_mean`	boolean (graphical parameter)
`bool_truncate_xaxis`	boolean (graphical parameter)
`bool_white_bg`	boolean (graphical parameter)
`bty`	character (graphical parameter)
`cex_axis`	positive number (graphical parameter)
`cex_gene_highlight_inner`	positive number (graphical parameter)
`cex_gene_highlight_outer`	positive number (graphical parameter)
`cex_lab`	positive number (graphical parameter)
`cex_points`	positive number (graphical parameter)
`col_points`	character for a color (graphical parameter)
`col_gene_highlight`	character for a color (graphical parameter)
`col_gene_highlight_border`	character for a color (graphical parameter)
`col_grid`	character for a color (graphical parameter)
`density`	positive number, `NA`, or `NULL` (graphical parameter)
`gene_names`	vector of charaters for which genes (in `names(rsquare_vec)`) to highlight
`lty_grid_major`	positive number (graphical parameter)
`lty_grid_minor`	positive number (graphical parameter)
`lty_polygon`	positive number (graphical parameter)
`lwd_axis`	positive number (graphical parameter)
`lwd_axis_ticks`	positive number (graphical parameter)
`lwd_grid_major`	positive number (graphical parameter)
`lwd_grid_minor`	positive number (graphical parameter)
`lwd_polygon`	positive number (graphical parameter)
`lwd_polygon_bold`	positive number (graphical parameter)
`mark_median_xthres`	boolean (graphical parameter)
`pch`	positive integer (graphical parameter)
`xaxt_num_ticks`	positive integer (graphical parameter)
`xaxt_grid_spacing`	positive integer (graphical parameter)
`xlab`	character (graphical parameter)
`xlim`	vector of 2 numerics, or `NULL` (graphical parameter)
`yaxt_by`	positive number (graphical parameter)
`yaxt_num_ticks`	positive integer (graphical parameter)
`ylab`	character (graphical parameter)
`ylim`	vector of 2 numerics, or `NULL` (graphical parameter)
`verbose`	non-negative integer
`...`	extra arguments to `graphics::plot`