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
...

Value

makes a plot but does not return anything