rotate_coordinates: Rotate numeric coordinates

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

Rotate numeric coordinates

Description

Rotate numeric coordinates, optionally after reflecting coordinates along one or more coordinate axes.

Usage

rotate_coordinates(
  x,
  degrees = 0,
  reflect = c("none", "x", "y", "z"),
  center = NULL,
  center_rule = c("median", "origin", "mean", "min", "max"),
  rotation_axes = c(1, 2),
  verbose = FALSE,
  ...
)

Arguments

x	matrix with 2 or more columns.
degrees	numeric value indicating the degrees to rotate layout coordinates, where 360 degrees is one complete rotation.
reflect	character string indicating one or more axes to reflect coordinates, which flips the position of coordinates along that axis. It is usually called to flip x-axis or y-axis coordinates, for example with reflect="x" or reflect=1. Input is handled as follows: if reflect contains "none", then reflect is applied to none of the coordinate axes, therefore the default reflect=c("none", "x", "y", "z") will apply no reflection. character input: reflect values are matched to colnames(x). When there are no colnames(x), then reflect values of c("x", "y", "z") are automatically recognized as columns c(1, 2, 3) respectively. integer input is treated as a vector of column index positions, for example reflect=c(2) will reflect values on the second coordinate column.
center	numeric coordinates to use as the center, or center=NULL to calculate the center using center_rule.
center_rule	character string indicating which rule to apply to determine the center coordinates when center=NULL. Note that it has little effect on most downstream plotting assuming the plot function adjusts x- and y-axis ranges to the data range, but may modify the axis ranges as a result. "origin" uses c(0, 0); "mean" uses the mean of each axis; "median" uses the median of each axis; "min" uses the minimum of each axis; "max" uses the max of each axis.
rotation_axes	integer vector indicating which axis coordinates to rotate, by default c(1, 2) uses the first two axes in x. Note that rotation_axes must represent columns present in x.
...	additional arguments are ignored.

Details

This function rotates coordinates in two axes, by the angle defined in degrees. It optionally reflects coordinates in one or more axes, which occurs before rotation.

Note that the reflect is applied before degrees.

Rotation code kindly contributed by Don MacQueen to the maptools package, and is reproduced here to avoid a dependency on maptools and therefore the sp package.

Value

⁠numeric matrix⁠ with the same number of columns as the input x.

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_legend_bivariate(), make_point_hull(), mem_find_overlap(), order_colors(), rank_mem_clusters(), subgraph_jam(), subset_mem(), summarize_node_spacing(), xyAngle()

Examples

layout <- cbind(0:10, 0:10);
layout_rot50 <- rotate_coordinates(x=layout, degrees=50);
layout_rot40_ctrmean <- rotate_coordinates(x=layout, degrees=40, center_rule="mean");
layout_reflectx_ctrmean <- rotate_coordinates(x=layout, reflect="x", center_rule="mean");
plot(rbind(layout, layout_rot50, layout_rot40_ctrmean, layout_reflectx_ctrmean),
   col=rep(c("darkorchid", "darkorange1", "dodgerblue", "red4"), each=11),
   pch=rep(c(17, 20, 18, 17), each=11),
   cex=2);

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