adjust_polygon_border: Adjust polygon border to inner or outer edge

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

Adjust polygon border to inner or outer edge

Description

Adjust polygon border to inner or outer edge

Usage

adjust_polygon_border(
  x,
  y = NULL,
  type = "inner",
  lwd_inch = 1/96,
  inner_cex = 1.001,
  lwd = par("lwd"),
  lwd_buffer = 0,
  verbose = FALSE,
  ...
)

Arguments

x	numeric polygon coordinates along the x-axis. Multiple polygons can be supplied by separating each polygon with NA, similar to how polygon() breaks coordinates into separate polygons at the position of missing values.
y	numeric polygon coordinates along the x-axis.
type	character string indicating where the border will be displayed: "inner": the polygon is shrunk by half the border line width "outer": the polygon is expanded by half the border line width
lwd_inch	numeric conversion of line width lwd units per inch, by default lwd=1 is defined as 1/96 inch.
inner_cex	numeric minor adjustment to calculations
lwd	numeric to define the intended line width for the resulting polygon border. By default it uses par("lwd").
...	additional arguments are ignored.

Details

This function intends to allow displaying a polygon border where the line itself only covers the inner or outer edge of the border itself. As a result, each polygon border for two adjacent polygons can be displayed without overlapping the other.

Value

list with elements x and y representing adjusted polygon coordinates. In the event that input x and y coordinates represent multiple polygons, the output x and y will also have NA values positioned between each polygon.

See Also

Other jam plot functions: grid_with_title(), jam_igraph(), mem_enrichment_heatmap(), mem_gene_path_heatmap(), mem_legend(), mem_multienrichplot(), mem_plot_folio(), plot_layout_scale()

Examples

a <- head(seq(from=0, to=360, length.out=6), 3) + 90;
xl <- round(10 * c(cos(a/180 * pi) * 5, 0)) / 10;
y <- round(10 * sin(a/180 * pi) * 5 / 10);
y <- y - min(y);
yl <- c(y, y[3]);
xr <- xl * -1;
yr <- yl;
lwdl <- 6;
lwdr <- 6;
lwdo <- 5;
par("ljoin"="mitre",
   "lend"="round",
   "mar"=c(3, 3, 1, 1))
plot(NULL, bty="L",
   xlim=c(-5, 30), ylim=c(-15, 10),
   #xlim=c(20, 30), ylim=c(0, 10),
   type="n", asp=1, xlab="", ylab="")
abline(h=c(0, -15), lwd=0.5, col="black", xpd=FALSE)

polygon(x=xl, y=yl,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xr, y=yr,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
jamba::drawLabels(x=0, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: Two adjacent polygon\nborders overlap.")

xy2l <- adjust_polygon_border(x=xl, y=yl, type="inner", lwd=lwdl)
xy2r <- adjust_polygon_border(x=xr, y=yr, type="inner", lwd=lwdr)

# draw properly resized polygon with inner border
polygon(x=xy2l$x + 25, y=xy2l$y,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 25, y=xy2r$y,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
jamba::drawLabels(x=25, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Adjust polygons so adjacent\ninner borders are both visible.")

# draw border around the pentagon
# except notice the border also overlaps the original polygon borders
polygon(x=xy2l$x, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
xy <- list(x=c(head(xl, 3), rev(head(xr, 3))),
   y=c(head(yl, 3), rev(head(yr, 3))) - 15)
polygon(x=xy$x, y=xy$y, col=NA, border="gold", lwd=lwdo)
jamba::drawLabels(x=0, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: The overall polygon border\noverlaps the inner polygon borders.")

# adjust for outer border
xy2 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo)
# draw properly resized polygon with inner border
polygon(x=xy2l$x + 25, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 25, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
# now draw outer border
polygon(x=xy2$x + 25, y=xy2$y,
   col=NA, border="gold", lwd=lwdo)
jamba::drawLabels(x=25, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Both the inner and outer\nborders are visible.")


# another example using different border line widths
lwdl <- 10;
lwdr <- 5;
lwdo <- 6;
plot(NULL, bty="L",
   xlim=c(-5, 30), ylim=c(-15, 10),
   type="n", asp=1, xlab="", ylab="")
abline(h=c(0, -15), lwd=0.5, col="black", xpd=FALSE)

polygon(x=xl, y=yl,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xr, y=yr,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
jamba::drawLabels(x=0, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: Two adjacent borders\noverlap, and the line widths\nare not aligned.")

xy2l <- adjust_polygon_border(x=xl, y=yl, type="inner", lwd=lwdl)
xy2r <- adjust_polygon_border(x=xr, y=yr, type="inner", lwd=lwdr)

# draw properly resized polygon with inner border
polygon(x=xy2l$x + 25, y=xy2l$y,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 25, y=xy2r$y,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
jamba::drawLabels(x=25, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Inner borders are both visible\nand well-aligned.")

# draw border around the pentagon
# except notice the border also overlaps the original polygon borders
polygon(x=xy2l$x, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
xy <- list(x=c(head(xl, 3), rev(head(xr, 3))),
   y=c(head(yl, 3), rev(head(yr, 3))) - 15)
polygon(x=xy$x, y=xy$y, col=NA, border="gold", lwd=lwdo)
jamba::drawLabels(x=0, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: The overall border still\noverlaps the inner polygon borders.")

# adjust for outer border
xy2 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo)
# draw properly resized polygon with inner border
polygon(x=xy2l$x + 25, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 25, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
# now draw outer border
polygon(x=xy2$x + 25, y=xy2$y,
   col=NA, border="gold", lwd=lwdo)
jamba::drawLabels(x=25, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: The inner and outer\nborders are all visible.")


# final example showing how to draw an additional border
lwdl <- 10;
lwdr <- 5;
lwdo <- 6;
plot(NULL, bty="L",
   xlim=c(-5, 30), ylim=c(-15, 10),
   type="n", asp=1, xlab="", ylab="")
abline(h=c(0, -15), lwd=0.5, col="black", xpd=FALSE)

# vanilla polygon border
polygon(x=xy$x, y=xy$y + 15,
   col="indianred3", border="darkorchid4", lwd=lwdo)
jamba::drawLabels(x=0, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: A vanilla polygon is drawn,\nwe want to add a border.")
# draw the same polygon
polygon(x=xy$x + 25, y=xy$y + 15,
   col="indianred3", border="darkorchid4", lwd=lwdo)
# add another outer border
xy3 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo,
   lwd_buffer=lwdo / 2)
polygon(x=xy3$x + 25, y=xy3$y + 15,
   col=NA, border="skyblue", lwd=lwdo)
xy4 <- adjust_polygon_border(x=xy$x, y=xy$y, type="inner", lwd=lwdo,
   lwd_buffer=lwdo / 2)
polygon(x=xy4$x + 25, y=xy4$y + 15,
   col=NA, border="yellow", lwd=lwdo)
jamba::drawLabels(x=25, y=10, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Use 'lwd_buffer' to adjust\nfor the existing border line width.")

# more complicated example with inner and outer borders
# draw properly resized polygon with inner border
polygon(x=xy2l$x, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
# now draw outer border
xy5 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo)
polygon(x=xy5$x, y=xy5$y,
   col=NA, border="skyblue", lwd=lwdo)
jamba::drawLabels(x=0, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: A polygon with inner and\nouter borders is drawn,\nwe want to add more borders.")

# draw same polygons
polygon(x=xy2l$x + 25, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 25, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
polygon(x=xy5$x + 25, y=xy5$y,
   col=NA, border="skyblue", lwd=lwdo)
# add inner borders
xy6 <- adjust_polygon_border(x=xl, y=yl, type="inner", lwd=lwdl,
   lwd_buffer=lwdl)
# note col="#FFFFFF01" is required for the final sharp polygon corner
polygon(x=c(xy6$x, xy6$x[c(0)]) + 25,
   y=c(xy6$y, xy6$y[c(0)]) - 15,
   col="#FFFFFF01", border="yellow", lwd=lwdl)
points(x=c(xy6$x, xy6$x[c(0)]) + 25,lend="butt",
   y=c(xy6$y, xy6$y[c(0)]) - 15,
   pch=as.character(seq_along(c(xy6$x, xy6$x[c(0)]))),
   col="black", cex=0.5)
xy7 <- adjust_polygon_border(x=xr, y=yr, type="inner", lwd=lwdr,
   lwd_buffer=lwdr)
polygon(x=c(xy7$x, xy7$x[c(0)]) + 25,
   y=c(xy7$y, xy7$y[c(0)]) - 15,
   col="#FFFFFF01", border="yellow", lwd=lwdr)
# new outer border
xy8 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo,
   lwd_buffer=lwdo)
polygon(x=xy8$x + 25, y=xy8$y,
   col="#FFFFFF01", border="red", lwd=lwdo)
jamba::drawLabels(x=25, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Use 'lwd_buffer' with\nproper line widths.\n(red and yellow)")

# show the effect of col=NA
plot(NULL, bty="L",
   xlim=c(-10, 25), ylim=c(-15, -5),
   type="n", asp=1, xlab="", ylab="")
abline(h=c(0, -15), lwd=0.5, col="black", xpd=FALSE)
# note that adjusted borders must be recalculated for new xlim,ylim
xy2l <- adjust_polygon_border(x=xl, y=yl, type="inner", lwd=lwdl)
xy2r <- adjust_polygon_border(x=xr, y=yr, type="inner", lwd=lwdr)
xy5 <- adjust_polygon_border(x=xy$x, y=xy$y, type="outer", lwd=lwdo)
# draw polygons
polygon(x=xy2l$x, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
polygon(x=xy5$x, y=xy5$y,
   col=NA, border="skyblue", lwd=lwdo)
polygon(x=xy2l$x + 15, y=xy2l$y - 15,
   col="indianred3", border="navy", lwd=lwdl)
polygon(x=xy2r$x + 15, y=xy2r$y - 15,
   col="dodgerblue", border="darkorchid3", lwd=lwdr)
polygon(x=xy5$x + 15, y=xy5$y,
   col=NA, border="skyblue", lwd=lwdo)
# add inner borders
xy6 <- adjust_polygon_border(x=xl, y=yl, type="inner", lwd=lwdl*2,
   lwd_buffer=lwdl)
# note col="#FFFFFF01" is required for the final sharp polygon corner
polygon(x=c(xy6$x, xy6$x[c(0)]) + 0,
   y=c(xy6$y, xy6$y[c(0)]) - 15,
   col=NA, border="yellow", lwd=lwdl*2)
polygon(x=c(xy6$x, xy6$x[c(0)]) + 15,
   y=c(xy6$y, xy6$y[c(0)]) - 15,
   col="#FFFFFF01", border="yellow", lwd=lwdl*2)
jamba::drawLabels(x=0, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Problem: Using col=NA causes the polygon corner\nto be 'ended', not 'joined'.")
jamba::drawLabels(x=15, y=-5, adjPreset="top",
   drawBox=FALSE,
   labelCex=0.8,
   txt="Solution: Use col='#FFFFFF01' to force\nproper sharp polygon corners.")



# example with multiple polygons vectorized
# generate an n-pointed star
n <- 3;
stars <- lapply(seq_len(n), function(i){
   angle <- seq(from=(i-1)*pi*2/n, to=i*pi*2/n, length=3);
   angle <- c(angle, angle[c(1, 1)], NA) + (n-2) * pi/(n * 2);
   xp <- cos(angle) * c(1, 2, 1, 0, 1, 1)
   yp <- sin(angle) * c(1, 2, 1, 0, 1, 1)
   cbind(x=xp, y=yp)
})
star_colors <- colorjam::rainbowJam(n)
plot(NULL, bty="L",
   type="n", asp=1, xlim=c(-2, 7), ylim=c(-6, 2.2),
   xlab="", ylab="")
polygon(jamba::rbindList(stars),
   col=jamba::alpha2col(star_colors, alpha=0.5),
   border=star_colors,
   lwd=10)
points(jamba::rbindList(stars), pch=20)
jamba::drawLabels(x=0, y=-1.5, adjPreset="bottom",
   drawBox=FALSE,
   labelCex=0.8,
   txt=paste0("Problem: Base R polygons\n",
      "have overlapping borders.\n",
      "Black points show each corner."))

stars_xy <- jamba::rbindList(stars)
stars_xy[,1] <- stars_xy[,1] + 5;
stars_xy_inner <- adjust_polygon_border(x=stars_xy, lwd=10)
polygon(stars_xy_inner,
   col=jamba::alpha2col(star_colors, alpha=0.5),
   border=star_colors,
   lwd=10)
jamba::drawLabels(x=5, y=-1.5, adjPreset="bottom",
   drawBox=FALSE,
   labelCex=0.8,
   txt=paste0("Solution: Polygon inner borders\n",
      "display each border color.\n",
      "And the triangle is properly sized!)"))

stars_xy_inner[[2]] <- stars_xy_inner[[2]] - 5;
polygon(x=jamba::rbindList(stars)[,1] + 5,
   y=jamba::rbindList(stars)[,2] - 5,
   col="white",
   border="black",
   lwd=2)
polygon(stars_xy_inner,
   col=jamba::alpha2col(star_colors, alpha=0.5),
   border=star_colors,
   lwd=10)
# the inner border adjustment can be vectorized
stars_xy_inner2 <- adjust_polygon_border(x=stars_xy_inner[[1]],
   y=stars_xy_inner[[2]], lwd=5, lwd_buffer=5)
polygon(stars_xy_inner2,
   col=NA,
   border="#FFFFEE88",
   lwd=5)

jmw86069/multienrichjam documentation built on Feb. 7, 2024, 12:58 a.m.