Display colors from bivariate color function

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.

Value

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

Details

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

See also

Other jam utility functions: ashape(), avg_angles(), avg_colors_by_list(), bulk_cnet_adjustments(), call_fn_ellipsis_deprecated(), cell_fun_bivariate(), collapse_mem_clusters(), colorRamp2D(), deconcat_df2(), display_colorRamp2D(), enrichList2geneHitList(), filter_mem_genes(), filter_mem_sets(), find_colname(), find_enrich_colnames(), 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)