make_legend_bivariate: Display colors from bivariate color function

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Display colors from bivariate color function

Description

Display colors from bivariate color function

Usage

make_legend_bivariate(
  col_fun,
  pretty.n = 5,
  name = "bivariate",
  xlab = "",
  ylab = "",
  title = "",
  border = TRUE,
  digits = 3,
  title_fontsize = 11,
  legend_fontsize = 10,
  grid_height = grid::unit(5, "mm"),
  grid_width = grid_height,
  row_breaks = NULL,
  column_breaks = NULL,
  row_gap = grid::unit(0, "mm"),
  column_gap = grid::unit(0, "mm"),
  ...
)

Arguments

col_fun	function as defined by colorRamp2D().
pretty.n	numeric value passed to pretty() to help define a suitable number of labels for the x-axis and y-axis color breaks. For specific breaks, use column_breaks, or row_breaks.
name	character string used to name the resulting ComplexHeatmap::Legend object, normally only useful when trying to find the grid object for custom modifications.
xlab, ylab	character strings used to define x-axis and y-axis labels, effectively the units being displayed. The common values should be xlab="z-score" or ⁠xlab="direction'⁠, and ylab="-log10pvalue" or y="log10 significance".
title	character, currently ignored, but may be used in future if necessary to display a title above the overall bivariate legend.
border	logical indicating whether to draw a border around each color square in the color legend. This argument can also be a character R color value, which will define the color of border drawn around each color square.
digits	numeric passed to format() to define the labels displayed at each position.
title_fontsize, legend_fontsize	numeric value passed to grid::gpar(fontsize) to define the font sizes for legend axis labels, and numerical legend labels, respectively.
grid_height, grid_width	grid::unit() objects to define the exact height and width of each colored square in the color legend.
row_breaks, column_breaks	numeric optional vectors which define absolute breaks for row and column values displayed in the color legend. When not supplied, these values are defined using pretty and argument pretty.n.
row_gap, column_gap	grid::unit() object to define optional visible gaps between color squares in the color legend. By default, there is no gap. These arguments are provided as a convenient way to impose a gap, since the method used does not otherwise provide a reasonable way to adjust the spacing.
...	additional arguments are ignored.

Details

This function produces a "Legend" object as defined by ComplexHeatmap::Legend().

Value

ComplexHeatmap::Legends-class object as returned by ComplexHeatmap::packLegend(), specifically containing a group of legends, otherwise known as a legend list.

See Also

Other jam utility functions: avg_angles(), avg_colors_by_list(), call_fn_ellipsis_deprecated(), cell_fun_bivariate(), collapse_mem_clusters(), colorRamp2D(), deconcat_df2(), display_colorRamp2D(), enrichList2geneHitList(), filter_mem_genes(), filter_mem_sets(), find_colname(), get_hull_data(), get_igraph_layout(), gsubs_remove(), handle_igraph_param_list(), isColorBlank(), make_point_hull(), mem_find_overlap(), order_colors(), rank_mem_clusters(), rotate_coordinates(), subgraph_jam(), subset_mem(), summarize_node_spacing(), xyAngle()

Examples

mcolor <- matrix(ncol=3,
   c("white", "salmon1", "firebrick3",
      "white", "lightgoldenrod1", "gold",
      "white", "skyblue", "dodgerblue3"));
row_breaks <- c(0, 0.5, 5);
column_breaks <- c(-1, 0, 1);
rownames(mcolor) <- row_breaks;
colnames(mcolor) <- column_breaks;
jamba::imageByColors(mcolor);

col_fun <- colorRamp2D(column_breaks=column_breaks,
   row_breaks=row_breaks,
   mcolor=mcolor)
lgds <- make_legend_bivariate(col_fun,
   ylab="-log10pvalue",
   xlab="z-score",
   pretty.n=5);
jamba::nullPlot(doBoxes=FALSE);
ComplexHeatmap::draw(lgds)

# same as above with slightly larger grid size
# and slightly larger font sizes
lgds <- make_legend_bivariate(col_fun,
   ylab="-log10pvalue",
   xlab="z-score",
   title_fontsize=14,
   legend_fontsize=12,
   grid_height=grid::unit(7, "mm"),
   pretty.n=5);
jamba::nullPlot(doBoxes=FALSE);
ComplexHeatmap::draw(lgds)

lgds <- make_legend_bivariate(col_fun,
   ylab="-log10pvalue",
   xlab="z-score",
   pretty.n=NULL);
jamba::nullPlot(doBoxes=FALSE);
ComplexHeatmap::draw(lgds)

lgds <- make_legend_bivariate(col_fun,
   ylab="-log10pvalue",
   xlab="z-score",
   column_breaks=c(-1, -0.5,  0, 0.5, 1),
   row_breaks=c(0, 0.25, 0.5, 0.75, 1),
   column_gap=grid::unit(1, "mm"),
   row_gap=grid::unit(1, "mm"),
   pretty.n=5);
jamba::nullPlot(doBoxes=FALSE);
ComplexHeatmap::draw(lgds)

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.