col_linear_xf: Linear color interpolation function with adjustable range,...
In jmw86069/colorjam: Jam Color manipulation functions

col_linear_xf

R Documentation

Linear color interpolation function with adjustable range, baseline, and floor

Description

Linear color interpolation function with adjustable range, baseline, and floor

Usage

col_linear_xf(
  x = 1,
  floor = 0,
  baseline = 0,
  lens = 0,
  n = 6,
  colramp = "Purples",
  open_floor = FALSE,
  debug = FALSE,
  ...
)

Arguments

`x`	`numeric` value used as a threshold, where numeric values at or above this value `x` are assigned the last color in the color gradient. Negative values at or below this negative value `-x` are assigned the first color in the color gradient.
`floor`	`numeric` optional value where numeric values between `-x` and `x` are assigned the middle color in the color gradient. Note that values at exactly `x` or `-x` are assigned the next respective color away from the middle color. When `floor=0` or `floor=NULL` no floor is applied, and colors are assigned using a continuous range of numeric values from `-x` to `x` with length `n`.
`baseline`	`numeric` value to define the baseline value, used when zero is not the initial value. Note that `baseline` can be either higher or lower than `x`, and colors from `colramp` will be applied starting at `baseline` through `x`.
`lens`	`numeric` value indicating a color lens applied to the color gradient, passed to `jamba::getColorRamp()`. Lens values `lens > 0` will condense the color gradient, making smaller changes more visually distinct; `lens < 0` expands the color gradient, making smaller changes less visually distinct.
`n`	`integer` number of colors used for the initial color gradient. This value is forced to be an odd number, so the "middle color" will always be represented as one strict color. Note that when using a `floor`, the first non-middle color is used for the `floor` assignment which means a smaller `n` value will assign a more visibly distinct color than using a larger `n`. See examples.
`colramp`	`character` passed to `jamba::getColorRamp()` which recognizes one of several forms of input: `character` string matching the name of a color ramp from `RColorBrewer` (see divergent palettes with `RColorBrewer::display.brewer.all(type="div")`). Note that adding `"_r"` will reverse the color gradient, so the default `"BuRd_r"` will create a color gradient with "blue-white-red" - with red for high values consistent with "heat" in "heatmaps" - where heat is red. `character` vector of R colors, which define a specific color ramp. This vector will be expanded to `n` length.
`open_floor`	`logical` indicating whether colors below the assigned `floor` will still receive non-middle color. Setting `open_floor=TRUE` is the best method to compare the effect of assigning the strict middle-color to values below the `floor`, versus using gradient colors below the `floor`, while all remaining numeric-color assignments are held constant.
`debug`	`logical` indicating whether to produce a plot that shows the resulting color gradient.
`...`	additional arguments are ignored.

Details

This function is the linear equivalent of col_div_xf(), in that it takes linear/sequential color gradient instead of a divergent color gradient.

Examples

col_fn1 <- col_linear_xf(x=3, baseline=0, floor=0)
col_fn2 <- col_linear_xf(x=3, baseline=0, floor=1)

col_fn2o <- col_linear_xf(x=3, baseline=0, floor=1, open_floor=TRUE)

test_seq <- seq(from=0, to=3, by=0.05);
names(test_seq) <- round(test_seq, digits=2);

opar <- par("mfrow"=c(1, 1));
bp0 <- barplot(abs(test_seq),
   las=2, yaxt="n",
   main="floor=0",
   col=col_fn1(test_seq),
   border="#22222222")
abline(v=bp0[abs(test_seq) == 1,], lty="dashed")
bp1 <- barplot(abs(test_seq),
   las=2, yaxt="n",
   main="floor=1",
   col=col_fn2(test_seq),
   border="#22222222")
abline(v=bp1[abs(test_seq) == 1,], lty="dashed")
bp2 <- barplot(abs(test_seq),
   las=2, yaxt="n",
   main="floor=1\nopen_floor=TRUE",
   col=col_fn2o(test_seq),
   border="#22222222")
abline(v=bp2[abs(test_seq) == 1,], lty="dashed")
par(opar)

col_fn3 <- col_linear_xf(x=3, baseline=6, floor=5)
test_seq <- seq(from=0, to=7, by=0.1);
names(test_seq) <- round(test_seq, digits=2);
bp3 <- barplot(abs(test_seq),
   las=2, yaxt="n",
   main="baseline=6, x=3, floor=5",
   col=col_fn3(test_seq),
   border="#22222222")
abline(v=bp3[abs(test_seq) == 5,], lty="dashed")
abline(v=bp3[abs(test_seq) == 3,], lty="dashed")

# Optionally show how to display data and legend in ComplexHeatmap
if (jamba::check_pkg_installed("ComplexHeatmap")) {
   set.seed(123);
   m <- abs(matrix(ncol=9, rnorm(81) * 8));
   col1 <- col_linear_xf(14, floor=4, n=8, lens=2);
   hm_1 <- ComplexHeatmap::Heatmap(m, col=col1,
      cell_fun=jamba::cell_fun_label(m=m, col_hm=col1),
      heatmap_legend_param=list(
         color_bar="discrete",
         at=c(0, 2, 3.99, 4, 6, 8, 10, 12, 14),
         border=TRUE),
      column_title="col_linear_xf(14, floor=4)",
      name="color key 1",
      border=TRUE);

   col2 <- col_linear_xf(14, floor=4, n=8, lens=2, open_floor=TRUE);
   hm_2 <- ComplexHeatmap::Heatmap(m,
      col=col2,
      cell_fun=jamba::cell_fun_label(m=m, col_hm=col2),
      heatmap_legend_param=list(
         color_bar="discrete",
         at=c(0, 2, 3.99, 4, 6, 8, 10, 12, 14),
         border=TRUE),
      column_title="col_linear_xf(14, floor=4, open_floor=TRUE)",
      name="color key 2",
      border=TRUE);
   hm_1 + hm_2
}

jmw86069/colorjam documentation built on March 18, 2024, 3:32 a.m.