R/jam_draw_contrasts.R
In jmw86069/jamses: Jam SummarizedExperiment Stats
#' Draw one-way contrast using block arrows
#'
#' Draw one-way contrast using block arrows
#'
#' @param x0,x1,y0,y1 `numeric` values with the start and end coordinates,
#' for the x and y axes, respectively.
#' @param color,border `character` R colors used to define color fill
#' and border, respectively, for each block arrow,
#' @param plot_type `character` string indicating the type of plot output:
#' * `"base"`: base R graphics
#' * `"grid"`: grid graphics (not yet implemented)
#' @param label `character` vector or `list` with optional label to
#' display atop each block arrow.
#' For base R graphics, the label is drawn using
#' `jamba::shadowText()` to render an outline around the text.
#' * When `label` is a `character` vector, it is converted to a `list`
#' in two ways depending upon the number of block arrows (`length(x0)`):
#' * `length == 1`: `label` is converted to `list` with length == 1.
#' * `length > 1`: `label` is converted to `list` using `as.list`,
#' then expanded to `length(x0)`.
#'
#' * When `label` is passed as a `list`, or after `label` is converted
#' to a `list`:
#'
#' * Each block arrow label uses one concatenated string after
#' calling `jamba::cPaste(..., sep=label_sep)` which joins values
#' by default using newline `"\n"` between each value.
#' @param label_sep `character` string used as separator, passed to
#' `jamba::cPaste()`, so that each block arrow may contain a vector
#' which is concatenated using `label_sep` between each value.
#' By default `label_sep="\n"` which prints each value on a new line.
#' @param na.rm `logical` passed to `jamba::cPaste()` to define how to
#' display NA labels:
#' * `na.rm=FALSE`: `"NA"`
#' * `na.rm=TRUE`: `""`.
#' @param label_color `character` color used for the `label`.
#' @param label_cex `numeric` label font expansion factor, used to adjust
#' the font size of the text label.
#' @param label_font `numeric` indicating the font face, defined as:
#' * 1 = normal font
#' * 2 = bold font
#' * 3 = italic font
#' * 4 = bold, italic font
#' @param do_plot `logical` indicating whether to draw the block arrow.
#' @param verbose `logical` indicating whether to print verbose output.
#' @param debug `logical` indicating whether to print additional debug info.
#' @param ... additional arguments are passed to `make_block_arrow_polygon()`,
#' including `arrow_ex` the arrow size expansion factor, and
#' `head_ex` the arrow head expansion factor, which is adjusted
#' relative to the arrow stem width.
#'
#' @examples
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_oneway_contrast(1, 4, 1, 1, label="contrast label")
#' draw_oneway_contrast(1, 4, 2, 2, head_ex=2, label_cex=1, label="contrast label")
#' draw_oneway_contrast(1, 4, 3, 3, arrow_ex=2, label_cex=2, label="contrast label")
#' draw_oneway_contrast(3, 0, 4, 1, arrow_ex=2, label_cex=2, label="contrast label")
#'
#' @export
draw_oneway_contrast <- function
(x0,
x1,
y0,
y1,
color="peachpuff",
border="black",
plot_type=c("base",
"grid"),
label=NULL,
label_sep="\n",
na.rm=TRUE,
label_color="white",
label_cex=1,
label_font=2,
oneway_position=0.5,
do_plot=TRUE,
verbose=FALSE,
debug=FALSE,
...)
{
# validate arguments
plot_type <- match.arg(plot_type);
# ensure vectorized values are proper lengths
n <- max(c(length(x0), length(x1), length(y0), length(y1)));
if (n == 0) {
# consider adding a warning
return(NULL)
}
x0 <- rep(x0, length.out=n)
x1 <- rep(x1, length.out=n)
y0 <- rep(y0, length.out=n)
y1 <- rep(y1, length.out=n)
# handle label argument
if (length(label) == 0) {
label <- rep(list(""), length.out=n);
}
# TODO: recognize color as list type,
# so each block arrow can use a gradient color fill.
# border should still be vector with length n, one border per block arrow.
if (n == 1) {
if (is.atomic(label)) {
label <- list(label)
}
} else if (is.atomic(label)) {
label <- as.list(label)
}
# define polygon coordinates
arrow_coords <- make_block_arrow_polygon(
x=x0,
x1=x1,
y=y0,
y1=y1,
data_format=plot_type,
# color=color,
# border=border,
...)
# render polygon(s)
if ("base" %in% plot_type) {
if (TRUE %in% do_plot) {
graphics::polygon(x=arrow_coords$x,
y=arrow_coords$y,
col=color,
border=border)
}
}
# optional text label
if (length(label) > 0) {
# ensure vectorized values are proper lengths
label <- rep(label, length.out=length(x0))
label_cex <- rep(label_cex, length.out=length(x0))
label_color <- rep(label_color, length.out=length(x0))
label_font <- rep(label_font, length.out=length(x0))
oneway_position <- rep(oneway_position, length.out=length(x0))
oneway_position <- jamba::noiseFloor(oneway_position,
minimum=0,
ceiling=1);
# base R graphics
if ("base" %in% plot_type) {
arrow_angle <- jamba::rad2deg(atan2(y=(y1 - y0), x=(x1 - x0))) %% 360;
# round to integer values
label_angle <- round(((arrow_angle + 90) %% 180 - 90) %% 360);
# label_angle <- arrow_angle;
angle_flip <- (arrow_angle != label_angle)
if (verbose) {
jamba::printDebug("draw_oneway_contrast(): ",
"x0: ", x0,
", x: ", (x0 + x1) / 2,
", x1: ", x1,
", y0: ", y0,
", y: ", (y0 + y1) / 2,
", y1: ", y1,
", arrow_angle: ", arrow_angle,
", label_angle: ", label_angle)
}
use_label <- jamba::cPaste(label,
sep=label_sep,
na.rm=TRUE)
which_labels <- which(!is.na(label) & nchar(label) > 0);
if (length(which_labels) > 0) {
# k_list <- split(which_labels, label_angle[which_labels])
label_split <- paste0(label_angle[which_labels], "_",
oneway_position[which_labels], "_",
as.character(angle_flip[which_labels]))
# print(data.frame(label_split, label_angle[which_labels], oneway_position[which_labels], which_labels));# debug
k_list <- split(which_labels, label_split)
# TODO: use jamba::drawLabels() with rotation and shadowText
# or gridtext::richtext_grob() with rounded corners and styling
for (k in k_list) {
use_oneway_position <- 1 - head(oneway_position[k], 1)
use_label_angle <- head(label_angle[k], 1);
use_arrow_angle <- head(arrow_angle[k], 1);
use_angle_flip <- head(angle_flip[k], 1);
use_adj <- c(
ifelse(use_angle_flip,
round(use_oneway_position * 2) / 2,
1 - (round(use_oneway_position * 2) / 2)),
0.5);
jamba::shadowText(
x=((x0 * ((1-oneway_position)*0.9 + 0.1) + x1 * (1 - ((1-oneway_position)*0.9 + 0.1))) )[k],
y=((y0 * ((1-oneway_position)*0.9 + 0.1) + y1 * (1 - ((1-oneway_position)*0.9 + 0.1))) )[k],
col=label_color[k],
srt=use_label_angle,
cex=label_cex[k],
alphaOutline=getOption("jam.alphaOutline", 0.95),
r=getOption("jam.shadow.r", 0.1),
n=getOption("jam.shadow.n", 8),
adj=use_adj,
font=label_font[k],
jamba::cPaste(label[k], sep="\n"))
if (debug) {
jamba::printDebug("use_adj:", use_adj,
", use_oneway_position:", use_oneway_position,
", use_label_angle:", use_label_angle,
", use_arrow_angle:", use_arrow_angle,
", use_angle_flip:", use_angle_flip,
", label[k]:", label[k]);# debug
}
}
}
} else if ("grid" %in% plot_type) {
# TODO: consider using shadowtext::grid.shadowtext()
}
}
return(invisible(arrow_coords));
}
#' Draw two one-way contrasts using block arrows, showing a two-way connector
#'
#' Draw two one-way contrasts using block arrows, showing a two-way connector
#'
#' This function essentially draws two one-way contrasts
#' in the form: `(group1-group2)-(group3-group4)`
#'
#' This two-way contrast is represented by two one-way contrasts:
#' 1. group1-group2
#' 2. group3-group4
#'
#' This function renders two individual one-way contrasts, then
#' draws a connector from the end of group2, to the beginning of group3.
#'
#' ## TODO:
#'
#' * Change the order of drawing:
#'
#' 1. Draw the two-way connector border.
#' 2. Draw the one-way contrasts.
#' 3. Draw the two-way connector fill.
#' 4. These steps would ensure the connector line does not
#' overlap the one-way contrasts, and would allow the connector to
#' connect directly to the contrast at the ends of the block arrows.
#'
#'
#' @inheritParams draw_oneway_contrast
#' @param extend_ex `numeric` which defines the amount to extend each
#' contrast arrow when defining control points for a bezier spline
#' from the end of one contrast, to the beginning of the next contrast.
#' The value `extend_ex` extends the contrast by 20% of the contrast
#' line length.
#' @param extend_angle `numeric` value in degrees (values from 0 to 360)
#' which defines the relative angle from the first contrast, toward
#' the second contrast, when defining control points for the bezier
#' spline. The default value `extend_angle=15` angles the extended line
#' 15 degrees toward the next contrast, starting at the end of the
#' first contrast. The same angle is used, rotated 180 degrees, for
#' the second control point at the beginning of the second contrast.
#' @param twoway_label `character` or `list` handled the same as `label`.
#' This label is placed atop the two-way connector, at an angle aligned
#' with the middle of the connector curved line.
#' @param twoway_label_color `character` color used for the `label`.
#' @param twoway_label_cex `numeric` label font expansion factor, used to adjust
#' the font size of the text label.
#' @param twoway_label_font `numeric` indicating the font face, defined as:
#' * 1 = normal font
#' * 2 = bold font
#' * 3 = italic font
#' * 4 = bold, italic font
#' @param twoway_position `numeric` value between 0 and 1 that places
#' the twoway label at this relative position along the two-way connector.
#' @param twoway_lwd `numeric` line width for the two-way connector.
#' @param contingency `character` string used to determine how to handle
#' the two-way connector in three practical scenarios. This argument
#' is expected to have length 3 with the following names, and is recycled
#' to this length as necesary:
#' * `"none"`: the bezier control points are sufficiently distant
#' that they do not cross the halfway line between contrasts.
#' * `"half"`: the bezier control point crosses the halfway line between
#' contrasts, but not the opposing contrast line. "Respect the halfieway."
#' * `"full"`: the bezier control point crosses the opposing contrast line,
#' which usually occurs when the two contrasts are rendered close to
#' one another.
#'
#' The value is used to define a contingency plan for each scenario above:
#' * `"none"`: the control points are used as-is with no contingency.
#' * `"scrunch"`: the `extend_angle` is reduced to 1/3, and the
#' control points are used as-is. This effectively makes the "S" swoop
#' narrower, so it fits between the two contrasts.
#' * `"loop"`: this option causes the two-way connector to loop from
#' contrast 1, around the far side of contrast 2.
#' The `extend_angle` and `extend_ex` is increased for contrast 1,
#' the `extend_angle` for contrast 2 is reversed, so the
#' bezier curve aims away from contrast 1.
#' When two contrasts are extremely close together, this technique
#' is the best method to make the line visible.
#' This option may provide suitable two-way labels which are not
#' obscured by intervening one-way conrasts.
#' @param draw_oneway `logical` indicating whether the one-way contrast
#' should be rendered, for example if the one-way contrast was
#' already rendered as part of another two-way contrast.
#' @param drawing_order `character` string indicating the overall order
#' for drawing plot features:
#' * `"two-two-one"`: draws the two-way border, two-way fill, then one-way
#' contrasts.
#' * `"one-two"`: draws the one-way contrasts, the two-way border,
#' then two-way fill.
#' * `"two-one-two"`: draws the two-way border, one-way contrasts, then
#' the two-way fill.
#' @param do_plot `logical` indicating whether to render the results in
#' the active graphics device, or when `do_plot=FALSE` only the underlying
#' data is returned with no plotting.
#'
#'
#' @examples
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 1), c(4, 4), c(1, 2), c(1, 2),
#' label=c("contrast one", "contrast two"))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 1), c(4, 4), c(1, 2), c(1, 2),
#' contingency=c("loop"),
#' label=c("contrast one", "contrast two"))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 2, 1, 2, 2, 2), c(4, 5, 4, 5, 5, 5),
#' c(1, 1.3, 2, 3, 4, 5), c(1, 1.3, 2, 3, 4, 5),
#' label=c("contrast one", "contrast two"),
#' extend_ex=0.5, extend_angle=10, color=colorjam::rainbowJam(6))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 2, 1, 2, 2, 2), c(4, 5, 4, 5, 5, 5),
#' c(1, 1.3, 2, 2.2, 4, 5), c(1, 1.3, 2, 2.2, 4, 5),
#' label=c("contrast one", "contrast two"),
#' extend_ex=0.3, extend_angle=20, color=colorjam::rainbowJam(6))
#'
#' plot(NULL, xlim=c(-2, 8), ylim=c(1, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(
#' x0=c(1, 2, 1, 2, 1, 1, 0, -2, 4, 3, 2, 4),
#' x1=c(4, 5, 4, 5, 6, 6, 0, -2, 7, 6, 2, 4),
#' y0=c(1, 1.3, 2, 2.2, 4, 5, 5, 5, 3.2, 3, 6, 6),
#' y1=c(1, 1.3, 2, 2.2, 4, 5, 3, 3, 3.2, 3, 3.5, 3.5),
#' label=c("contrast one", "contrast two"), verbose=TRUE,
#' extend_ex=0.5, extend_angle=10,
#' color=colorjam::rainbowJam(12, Crange=c(90, 120)))
#'
#' draw_twoway_contrast(x0=c(4, 3), x1=c(4, 3), y0=c(2, 2), y1=c(1, 1),
#' label=c("contrast one", "contrast two"),
#' color=c("gold", "dodgerblue"), extend_angle=-20)
#' @export
draw_twoway_contrast <- function
(x0,
x1,
y0,
y1,
color="peachpuff",
border="black",
extend_ex=0.3,
extend_angle=10,
plot_type=c("base",
"grid"),
label=NULL,
label_sep="\n",
na.rm=TRUE,
label_color="white",
label_cex=1,
label_font=2,
oneway_position=0.5,
twoway_label=NULL,
twoway_label_color=label_color,
twoway_label_cex=label_cex,
twoway_label_font=label_font,
twoway_position=0.5,
twoway_lwd=5,
contingency=c(none="none",
half="scrunch",
full="loop"),
draw_oneway=TRUE,
drawing_order=c(
"two-two-one",
"one-two",
"two-one-two"),
do_plot=TRUE,
verbose=FALSE,
...)
{
# validate arguments
plot_type <- match.arg(plot_type);
contingency <- match.arg(contingency,
several.ok=TRUE);
contingency_names <- c("none", "half", "full");
if (!all(contingency_names %in% contingency)) {
contingency <- rep(contingency, length.out=3);
names(contingency) <- contingency_names;
}
drawing_order <- match.arg(drawing_order);
# ensure vectorized values are proper lengths
n <- max(c(length(x0), length(x1), length(y0), length(y1)));
if (n == 0) {
# consider adding a warning
return(NULL)
}
x0 <- rep(x0, length.out=n)
x1 <- rep(x1, length.out=n)
y0 <- rep(y0, length.out=n)
y1 <- rep(y1, length.out=n)
color <- rep(color, length.out=n);
colorset_twoway <- split(color, rep(seq_len(n / 2), each=2))
border <- rep(border, length.out=n);
# first draw the two one-way contrasts
if (TRUE %in% draw_oneway && "one-two" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
do_plot=do_plot,
verbose=verbose,
...)
}
# index values for first and second contrast
k1 <- seq(from=1, to=length(x0), by=2)
k2 <- k1 + 1;
# determine the two-way connector
contrast_angles <- jamba::rad2deg(atan2(y=(y1 - y0),
x=(x1 - x0)));
# flip each second contrast
contrast_angles[k2] <- (contrast_angles[k2] + 180) %% 360
# determine handedness of the two contrasts
hand <- point_handedness(
pt1=cbind(c(x0[k1]), c(y0[k1])),
pt2=cbind(c(x0[k2]), c(y0[k2])),
angle=contrast_angles[k1])
if (verbose) {
jamba::printDebug("draw_twoway_contrast(): ",
"hand: ", hand);
}
contrast_lengths <- sqrt(
(x1 - x0)^2 + (y1 - y0)^2)
# helper function to make bezier control points
make_bezier_lines_df <- function
(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex,
xadj,
yadj)
{
# Note: using length=1 instead of contrast_lengths[k1]
extend_ex <- rep(extend_ex, length.out=length(x0));
# so the extension has consistent length.
lines_df <- data.frame(
x=c(
# x0=x0[k1],
`x0.5`=(x0[k1] +
x1[k1])/2,
`x0.75`=(x0[k1] +
x1[k1]*3)/4,
x1=x1[k1],
`x1.2`=(x1[k1] +
xadj[k1] * 1 * extend_ex[k1]),
`x1.5`=(x1[k1] +
x0[k2])/2,
`x1.8`=(x0[k2] +
xadj[k2] * 1 * extend_ex[k2]),
x2=x0[k2],
`x2.25`=(x0[k2]*3 +
x1[k2])/4,
`x2.5`=(x0[k2] +
x1[k2])/2),
# x3=x1[k2]),
y=c(
# y0=y0[k1],
`y0.5`=(y0[k1] +
y0[k1])/2,
`y0.75`=(y0[k1] +
y0[k1]*3)/4,
y1=y1[k1],
`x1.2`=(y1[k1] +
yadj[k1] * 1 * extend_ex[k1]),
`y1.5`=(y1[k1] +
y0[k2])/2,
`y1.8`=(y0[k2] +
yadj[k2] * 1 * extend_ex[k2]),
y2=y0[k2],
`y2.25`=(y0[k2]*3 +
y1[k2])/4,
`y2.5`=(y0[k2] +
y1[k2])/2)
);
return(lines_df);
}
# determine appropriate angle
angle_diff <- -(extend_angle);
angle_diff <- ifelse(rep(hand, each=2) %in% "right",
extend_angle,
-extend_angle)
new_contrast_angles <- contrast_angles + angle_diff;
if (verbose) {
jamba::printDebug("draw_twoway_contrast(): ",
"new_contrast_angles: ");
print(data.frame(contrast_angles, hand=rep(hand, each=2),
angle_diff, new_contrast_angles));
}
# optionally mirror the angle when lines are too close?
# mirror the first contrast? might be useful when lines are too close
# new_contrast_angles[k1] <- (360 - new_contrast_angles[k1]) %% 360;
# mirror the second contrast? might be useful when lines are too close
# new_contrast_angles[k2] <- (360 - new_contrast_angles[k2]) %% 360;
# new_contrast_angles <- (360 - new_contrast_angles) %% 360;
# jamba::printDebug("new_contrast_angles:", new_contrast_angles); # debug
xadj <- cos(jamba::deg2rad(new_contrast_angles))
yadj <- sin(jamba::deg2rad(new_contrast_angles))
# define bezier control points for typical cases
lines_df <- make_bezier_lines_df(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex=extend_ex,
xadj, yadj);
# check for weird cases:
# - when control point x1.2 crosses either the
# x1.5 (midpoint) or
# x2.5 (opposite contrast)
# - test whether "handedness" changes relative to those points
x12_rows <- jamba::igrep("^x1.2", rownames(lines_df));
x15_rows <- jamba::igrep("^x1.5", rownames(lines_df));
x25_rows <- jamba::igrep("^x2.5", rownames(lines_df));
new_hand_25 <- point_handedness(
pt1=as.matrix(lines_df[x12_rows, , drop=FALSE]),
pt2=as.matrix(lines_df[x25_rows, , drop=FALSE]),
angle=contrast_angles[k1])
new_hand_15 <- point_handedness(
pt1=as.matrix(lines_df[x12_rows, , drop=FALSE]),
pt2=as.matrix(lines_df[x15_rows, , drop=FALSE]),
angle=contrast_angles[k1])
# if it crosses x25, we should loop
# if it crosses x15 but not x25, maybe we scrunch
changed_hands_25 <- (hand != new_hand_25);
changed_hands_15 <- (hand != new_hand_15);
## summarize the contingency scenario, defined as:
# none - the control point does not cross the halfieway
# half - the control point crosses the halfieway, not the other contrast
# full - the control point crosses the other contrast
contingency_scenario <- ifelse(
!changed_hands_25 & !changed_hands_15, "none",
ifelse(changed_hands_25, "full", "half"))
contingency_output <- contingency[contingency_scenario]
# calculate two-way contrast distance between component one-way contrasts
calc_twoway_distance <- function
(x0, x1, y0, y1)
{
# calculate two-way distance
if (length(x1) < 2) {
return(NULL)
}
x1 <- rep(x1, length.out=length(x0));
y0 <- rep(y0, length.out=length(x0));
y1 <- rep(y1, length.out=length(x0));
xym <- cbind(c(x0, x1), c(y0, y1));
rownames(xym) <- jamba::makeNames(
rep(c("A", "B"), each=length(x0)),
suffix="_con")
xyseq <- rep(seq_along(x0), each=2) + c(0, length(x0))
xym1 <- xym[xyseq, , drop=FALSE]
xym1_split <- split(rownames(xym1),
rep(seq_len(length(x0)/2), each=4));
twoway_distances <- sapply(xym1_split, function(irows){
dm <- as.matrix(dist(xym1[irows, , drop=FALSE]))
acols <- grepl("con1", colnames(dm));
max(c(0.5,
min(dm[!acols, acols, drop=FALSE], na.rm=TRUE)))
})
return(twoway_distances)
}
# if (any(c(changed_hands_25, changed_hands_15))) {
twoway_distances <- calc_twoway_distance(x0, x1, y0, y1)
if (any(c("scrunch", "loop") %in% contingency_output)) {
# mirror the second angle?
# if (any(changed_hands_25)) {
extend_ex <- rep(extend_ex, length.out=length(contrast_angles))
do_loop <- ("loop" %in% contingency_output);
if (any(do_loop)) {
k1_changed <- k1[do_loop];
k2_changed <- k2[do_loop];
# extend_ex[k1_changed] <- extend_ex[k1_changed] * 5;
# extend_ex[k1_changed] <- 2;
extend_ex[k1_changed] <- twoway_distances[do_loop] + sqrt(twoway_distances[do_loop])/2;
# extend_ex[k2_changed] <- extend_ex[k2_changed] * 2;
extend_ex[k2_changed] <- sqrt(twoway_distances[do_loop]);
# extend_ex[k2_changed] <- twoway_distances[do_loop] / 1;
new_contrast_angles[k2_changed] <- (contrast_angles[k2_changed] -
# angle_diff) %% 360
angle_diff * sqrt(twoway_distances[do_loop])) %% 360
# new_contrast_angles[k2_changed] <- (360 -
# new_contrast_angles[k2_changed]) %% 360;
new_contrast_angles[k1_changed] <- (contrast_angles[k1_changed] +
60 * sign(angle_diff)) %% 360
}
# if (any(changed_hands_15 & !changed_hands_25)) {
do_scrunch <- ("scrunch" %in% contingency_output)
if (any(do_scrunch)) {
k1_changed <- k1[do_scrunch];
k2_changed <- k2[do_scrunch];
new_contrast_angles[k1_changed] <- (contrast_angles[k1_changed] +
angle_diff / 3);
new_contrast_angles[k2_changed] <- (contrast_angles[k2_changed] +
angle_diff / 3);
}
xadj <- cos(jamba::deg2rad(new_contrast_angles))
yadj <- sin(jamba::deg2rad(new_contrast_angles))
# define bezier control points for typical cases
lines_df <- make_bezier_lines_df(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex=extend_ex,
xadj, yadj);
}
# optionally adjust x1.5,y1.5 to be midpoint between x1.2-x1.8 and y1.2-y1.8
x12_rows <- jamba::igrep("^x1.2", rownames(lines_df));
x15_rows <- jamba::igrep("^x1.5", rownames(lines_df));
x18_rows <- jamba::igrep("^x1.8", rownames(lines_df));
lines_df[x15_rows, "x"] <- (lines_df[x12_rows, "x"] + lines_df[x18_rows, "x"]) / 2;
lines_df[x15_rows, "y"] <- (lines_df[x12_rows, "y"] + lines_df[x18_rows, "y"]) / 2;
# bezier::bezier() is not vectorized, so iterate each set of control points
k_multiple <- (length(x0) / 2)
# iterate to calculate each bezier curve
bezier_curves <- lapply(seq_len(k_multiple), function(k){
k_seq <- seq(from=k, length.out=9, by=k_multiple)
use_lines_df <- lines_df[k_seq, , drop=FALSE]
# optionally display the control points with labels for debugging
if (FALSE) {
points(use_lines_df,
pch=21,
cex=4,
col="grey",
bg="white")
text(use_lines_df, rownames(lines_df), pch=21, cex=0.8)
}
# calculate bezier curve
bezier_points <- bezier::bezier(
t=seq(from=0, to=4, length.out=100),
p=as.matrix(use_lines_df), deg=2)
bezier_points
})
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
if ("one-two" %in% drawing_order) {
ik <- 25:76
} else {
ik <- 24:76;
}
bezier_line_use <- bezier_points[ik, , drop=FALSE];
lines(bezier_line_use,
lwd=twoway_lwd + 2,
col=border[k * 2 - 1]);
}
# optionally draw one-way contrasts here
if (TRUE %in% draw_oneway && "two-one-two" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
}
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
if ("one-two" %in% drawing_order) {
ik <- 23:77;
} else {
ik <- 23:77;
}
# render thinner line with colored segments
bezier_use <- bezier_points[ik, , drop=FALSE];
graphics::segments(
x0=head(bezier_use, -1)[,1],
x1=tail(bezier_use, -1)[,1],
y0=head(bezier_use, -1)[,2],
y1=tail(bezier_use, -1)[,2],
col=jamba::getColorRamp(
# c("dodgerblue", "firebrick2"),
colorset_twoway[[k]],
n=nrow(bezier_use) - 1),
lwd=twoway_lwd)
}
# optionally draw one-way contrasts here
if (TRUE %in% draw_oneway && "two-two-one" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=NULL,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
# optional "flourish" to re-draw the start/end
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
ik <- 23:77;
# then take first 5, last 5 points
# render thinner line with colored segments
bezier_use <- bezier_points[ik, , drop=FALSE];
bezier_use_start <- head(bezier_use, 5);
bezier_use_end <- tail(bezier_use, 5);
bezier_colors <- jamba::getColorRamp(
colorset_twoway[[k]],
n=nrow(bezier_use) - 1);
graphics::segments(
x0=head(bezier_use_start, -1)[,1],
x1=tail(bezier_use_start, -1)[,1],
y0=head(bezier_use_start, -1)[,2],
y1=tail(bezier_use_start, -1)[,2],
col=head(bezier_colors, 5),
lwd=twoway_lwd)
graphics::segments(
x0=head(bezier_use_end, -1)[,1],
x1=tail(bezier_use_end, -1)[,1],
y0=head(bezier_use_end, -1)[,2],
y1=tail(bezier_use_end, -1)[,2],
col=tail(bezier_colors, 5),
lwd=twoway_lwd)
}
# last step is to draw labels so they are not covered by the bezier curve
# oneway labels
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=NA,
border=NA,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
# twoway labels
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# define where to place the label
kn <- floor(twoway_position * 50) + 25;
# grab points in the middle
klen <- 7;
kn_start <- min(c(max(c(kn - klen, 15)), 85 - klen * 2))
ik <- seq(kn_start, length.out=15);
kn <- floor(mean(ik));
# ik <- 43:57;
bezier_use <- bezier_points[ik, , drop=FALSE];
# optionally render thinner line with colored segments
# graphics::segments(
# x0=head(bezier_use, -1)[,1],
# x1=tail(bezier_use, -1)[,1],
# y0=head(bezier_use, -1)[,2],
# y1=tail(bezier_use, -1)[,2],
# col="grey25",
# lwd=twoway_lwd * 2)
vector_angle <- jamba::rad2deg(atan2(
y=(tail(bezier_use, 1)[, 2] - head(bezier_use, 1)[, 2]),
x=(tail(bezier_use, 1)[, 1] - head(bezier_use, 1)[, 1]))) %% 360;
# discretize the angles so nearly parallel labels are
# likely to be parallel
# (most noticeable when one is 91 and the other is 89,
# and the labels are flipped left/right)
vector_angle <- round(vector_angle / 22.5) * 22.5;
# jamba::printDebug("vector_angle:", vector_angle);# debug
# round to integer values
twoway_label_angle <- round(
((vector_angle + 90) %% 180 - 90) %% 360);
use_angle_flip <- (twoway_label_angle != vector_angle)
use_adj <- c(
ifelse(use_angle_flip,
1 - (round(twoway_position * 8) / 8),
round(twoway_position * 8) / 8),
0.5);
jamba::shadowText(
x=bezier_points[kn, 1],
y=bezier_points[kn, 2],
col=twoway_label_color,
srt=twoway_label_angle,
cex=twoway_label_cex,
alphaOutline=getOption("jam.alphaOutline", 0.95),
r=getOption("jam.shadow.r", 0.1),
n=getOption("jam.shadow.n", 8),
# adj=c(0.5, 0.5),
adj=use_adj,
font=twoway_label_font,
jamba::cPaste(twoway_label, sep="\n"))
}
}
invisible(NULL)
}
jmw86069/jamses documentation built on May 31, 2024, 1:36 p.m.
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#' Draw one-way contrast using block arrows
#'
#' Draw one-way contrast using block arrows
#'
#' @param x0,x1,y0,y1 `numeric` values with the start and end coordinates,
#' for the x and y axes, respectively.
#' @param color,border `character` R colors used to define color fill
#' and border, respectively, for each block arrow,
#' @param plot_type `character` string indicating the type of plot output:
#' * `"base"`: base R graphics
#' * `"grid"`: grid graphics (not yet implemented)
#' @param label `character` vector or `list` with optional label to
#' display atop each block arrow.
#' For base R graphics, the label is drawn using
#' `jamba::shadowText()` to render an outline around the text.
#' * When `label` is a `character` vector, it is converted to a `list`
#' in two ways depending upon the number of block arrows (`length(x0)`):
#' * `length == 1`: `label` is converted to `list` with length == 1.
#' * `length > 1`: `label` is converted to `list` using `as.list`,
#' then expanded to `length(x0)`.
#'
#' * When `label` is passed as a `list`, or after `label` is converted
#' to a `list`:
#'
#' * Each block arrow label uses one concatenated string after
#' calling `jamba::cPaste(..., sep=label_sep)` which joins values
#' by default using newline `"\n"` between each value.
#' @param label_sep `character` string used as separator, passed to
#' `jamba::cPaste()`, so that each block arrow may contain a vector
#' which is concatenated using `label_sep` between each value.
#' By default `label_sep="\n"` which prints each value on a new line.
#' @param na.rm `logical` passed to `jamba::cPaste()` to define how to
#' display NA labels:
#' * `na.rm=FALSE`: `"NA"`
#' * `na.rm=TRUE`: `""`.
#' @param label_color `character` color used for the `label`.
#' @param label_cex `numeric` label font expansion factor, used to adjust
#' the font size of the text label.
#' @param label_font `numeric` indicating the font face, defined as:
#' * 1 = normal font
#' * 2 = bold font
#' * 3 = italic font
#' * 4 = bold, italic font
#' @param do_plot `logical` indicating whether to draw the block arrow.
#' @param verbose `logical` indicating whether to print verbose output.
#' @param debug `logical` indicating whether to print additional debug info.
#' @param ... additional arguments are passed to `make_block_arrow_polygon()`,
#' including `arrow_ex` the arrow size expansion factor, and
#' `head_ex` the arrow head expansion factor, which is adjusted
#' relative to the arrow stem width.
#'
#' @examples
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_oneway_contrast(1, 4, 1, 1, label="contrast label")
#' draw_oneway_contrast(1, 4, 2, 2, head_ex=2, label_cex=1, label="contrast label")
#' draw_oneway_contrast(1, 4, 3, 3, arrow_ex=2, label_cex=2, label="contrast label")
#' draw_oneway_contrast(3, 0, 4, 1, arrow_ex=2, label_cex=2, label="contrast label")
#'
#' @export
draw_oneway_contrast <- function
(x0,
x1,
y0,
y1,
color="peachpuff",
border="black",
plot_type=c("base",
"grid"),
label=NULL,
label_sep="\n",
na.rm=TRUE,
label_color="white",
label_cex=1,
label_font=2,
oneway_position=0.5,
do_plot=TRUE,
verbose=FALSE,
debug=FALSE,
...)
{
# validate arguments
plot_type <- match.arg(plot_type);
# ensure vectorized values are proper lengths
n <- max(c(length(x0), length(x1), length(y0), length(y1)));
if (n == 0) {
# consider adding a warning
return(NULL)
}
x0 <- rep(x0, length.out=n)
x1 <- rep(x1, length.out=n)
y0 <- rep(y0, length.out=n)
y1 <- rep(y1, length.out=n)
# handle label argument
if (length(label) == 0) {
label <- rep(list(""), length.out=n);
}
# TODO: recognize color as list type,
# so each block arrow can use a gradient color fill.
# border should still be vector with length n, one border per block arrow.
if (n == 1) {
if (is.atomic(label)) {
label <- list(label)
}
} else if (is.atomic(label)) {
label <- as.list(label)
}
# define polygon coordinates
arrow_coords <- make_block_arrow_polygon(
x=x0,
x1=x1,
y=y0,
y1=y1,
data_format=plot_type,
# color=color,
# border=border,
...)
# render polygon(s)
if ("base" %in% plot_type) {
if (TRUE %in% do_plot) {
graphics::polygon(x=arrow_coords$x,
y=arrow_coords$y,
col=color,
border=border)
}
}
# optional text label
if (length(label) > 0) {
# ensure vectorized values are proper lengths
label <- rep(label, length.out=length(x0))
label_cex <- rep(label_cex, length.out=length(x0))
label_color <- rep(label_color, length.out=length(x0))
label_font <- rep(label_font, length.out=length(x0))
oneway_position <- rep(oneway_position, length.out=length(x0))
oneway_position <- jamba::noiseFloor(oneway_position,
minimum=0,
ceiling=1);
# base R graphics
if ("base" %in% plot_type) {
arrow_angle <- jamba::rad2deg(atan2(y=(y1 - y0), x=(x1 - x0))) %% 360;
# round to integer values
label_angle <- round(((arrow_angle + 90) %% 180 - 90) %% 360);
# label_angle <- arrow_angle;
angle_flip <- (arrow_angle != label_angle)
if (verbose) {
jamba::printDebug("draw_oneway_contrast(): ",
"x0: ", x0,
", x: ", (x0 + x1) / 2,
", x1: ", x1,
", y0: ", y0,
", y: ", (y0 + y1) / 2,
", y1: ", y1,
", arrow_angle: ", arrow_angle,
", label_angle: ", label_angle)
}
use_label <- jamba::cPaste(label,
sep=label_sep,
na.rm=TRUE)
which_labels <- which(!is.na(label) & nchar(label) > 0);
if (length(which_labels) > 0) {
# k_list <- split(which_labels, label_angle[which_labels])
label_split <- paste0(label_angle[which_labels], "_",
oneway_position[which_labels], "_",
as.character(angle_flip[which_labels]))
# print(data.frame(label_split, label_angle[which_labels], oneway_position[which_labels], which_labels));# debug
k_list <- split(which_labels, label_split)
# TODO: use jamba::drawLabels() with rotation and shadowText
# or gridtext::richtext_grob() with rounded corners and styling
for (k in k_list) {
use_oneway_position <- 1 - head(oneway_position[k], 1)
use_label_angle <- head(label_angle[k], 1);
use_arrow_angle <- head(arrow_angle[k], 1);
use_angle_flip <- head(angle_flip[k], 1);
use_adj <- c(
ifelse(use_angle_flip,
round(use_oneway_position * 2) / 2,
1 - (round(use_oneway_position * 2) / 2)),
0.5);
jamba::shadowText(
x=((x0 * ((1-oneway_position)*0.9 + 0.1) + x1 * (1 - ((1-oneway_position)*0.9 + 0.1))) )[k],
y=((y0 * ((1-oneway_position)*0.9 + 0.1) + y1 * (1 - ((1-oneway_position)*0.9 + 0.1))) )[k],
col=label_color[k],
srt=use_label_angle,
cex=label_cex[k],
alphaOutline=getOption("jam.alphaOutline", 0.95),
r=getOption("jam.shadow.r", 0.1),
n=getOption("jam.shadow.n", 8),
adj=use_adj,
font=label_font[k],
jamba::cPaste(label[k], sep="\n"))
if (debug) {
jamba::printDebug("use_adj:", use_adj,
", use_oneway_position:", use_oneway_position,
", use_label_angle:", use_label_angle,
", use_arrow_angle:", use_arrow_angle,
", use_angle_flip:", use_angle_flip,
", label[k]:", label[k]);# debug
}
}
}
} else if ("grid" %in% plot_type) {
# TODO: consider using shadowtext::grid.shadowtext()
}
}
return(invisible(arrow_coords));
}
#' Draw two one-way contrasts using block arrows, showing a two-way connector
#'
#' Draw two one-way contrasts using block arrows, showing a two-way connector
#'
#' This function essentially draws two one-way contrasts
#' in the form: `(group1-group2)-(group3-group4)`
#'
#' This two-way contrast is represented by two one-way contrasts:
#' 1. group1-group2
#' 2. group3-group4
#'
#' This function renders two individual one-way contrasts, then
#' draws a connector from the end of group2, to the beginning of group3.
#'
#' ## TODO:
#'
#' * Change the order of drawing:
#'
#' 1. Draw the two-way connector border.
#' 2. Draw the one-way contrasts.
#' 3. Draw the two-way connector fill.
#' 4. These steps would ensure the connector line does not
#' overlap the one-way contrasts, and would allow the connector to
#' connect directly to the contrast at the ends of the block arrows.
#'
#'
#' @inheritParams draw_oneway_contrast
#' @param extend_ex `numeric` which defines the amount to extend each
#' contrast arrow when defining control points for a bezier spline
#' from the end of one contrast, to the beginning of the next contrast.
#' The value `extend_ex` extends the contrast by 20% of the contrast
#' line length.
#' @param extend_angle `numeric` value in degrees (values from 0 to 360)
#' which defines the relative angle from the first contrast, toward
#' the second contrast, when defining control points for the bezier
#' spline. The default value `extend_angle=15` angles the extended line
#' 15 degrees toward the next contrast, starting at the end of the
#' first contrast. The same angle is used, rotated 180 degrees, for
#' the second control point at the beginning of the second contrast.
#' @param twoway_label `character` or `list` handled the same as `label`.
#' This label is placed atop the two-way connector, at an angle aligned
#' with the middle of the connector curved line.
#' @param twoway_label_color `character` color used for the `label`.
#' @param twoway_label_cex `numeric` label font expansion factor, used to adjust
#' the font size of the text label.
#' @param twoway_label_font `numeric` indicating the font face, defined as:
#' * 1 = normal font
#' * 2 = bold font
#' * 3 = italic font
#' * 4 = bold, italic font
#' @param twoway_position `numeric` value between 0 and 1 that places
#' the twoway label at this relative position along the two-way connector.
#' @param twoway_lwd `numeric` line width for the two-way connector.
#' @param contingency `character` string used to determine how to handle
#' the two-way connector in three practical scenarios. This argument
#' is expected to have length 3 with the following names, and is recycled
#' to this length as necesary:
#' * `"none"`: the bezier control points are sufficiently distant
#' that they do not cross the halfway line between contrasts.
#' * `"half"`: the bezier control point crosses the halfway line between
#' contrasts, but not the opposing contrast line. "Respect the halfieway."
#' * `"full"`: the bezier control point crosses the opposing contrast line,
#' which usually occurs when the two contrasts are rendered close to
#' one another.
#'
#' The value is used to define a contingency plan for each scenario above:
#' * `"none"`: the control points are used as-is with no contingency.
#' * `"scrunch"`: the `extend_angle` is reduced to 1/3, and the
#' control points are used as-is. This effectively makes the "S" swoop
#' narrower, so it fits between the two contrasts.
#' * `"loop"`: this option causes the two-way connector to loop from
#' contrast 1, around the far side of contrast 2.
#' The `extend_angle` and `extend_ex` is increased for contrast 1,
#' the `extend_angle` for contrast 2 is reversed, so the
#' bezier curve aims away from contrast 1.
#' When two contrasts are extremely close together, this technique
#' is the best method to make the line visible.
#' This option may provide suitable two-way labels which are not
#' obscured by intervening one-way conrasts.
#' @param draw_oneway `logical` indicating whether the one-way contrast
#' should be rendered, for example if the one-way contrast was
#' already rendered as part of another two-way contrast.
#' @param drawing_order `character` string indicating the overall order
#' for drawing plot features:
#' * `"two-two-one"`: draws the two-way border, two-way fill, then one-way
#' contrasts.
#' * `"one-two"`: draws the one-way contrasts, the two-way border,
#' then two-way fill.
#' * `"two-one-two"`: draws the two-way border, one-way contrasts, then
#' the two-way fill.
#' @param do_plot `logical` indicating whether to render the results in
#' the active graphics device, or when `do_plot=FALSE` only the underlying
#' data is returned with no plotting.
#'
#'
#' @examples
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 1), c(4, 4), c(1, 2), c(1, 2),
#' label=c("contrast one", "contrast two"))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 4), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 1), c(4, 4), c(1, 2), c(1, 2),
#' contingency=c("loop"),
#' label=c("contrast one", "contrast two"))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 2, 1, 2, 2, 2), c(4, 5, 4, 5, 5, 5),
#' c(1, 1.3, 2, 3, 4, 5), c(1, 1.3, 2, 3, 4, 5),
#' label=c("contrast one", "contrast two"),
#' extend_ex=0.5, extend_angle=10, color=colorjam::rainbowJam(6))
#'
#' plot(NULL, xlim=c(0, 5), ylim=c(0, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(c(1, 2, 1, 2, 2, 2), c(4, 5, 4, 5, 5, 5),
#' c(1, 1.3, 2, 2.2, 4, 5), c(1, 1.3, 2, 2.2, 4, 5),
#' label=c("contrast one", "contrast two"),
#' extend_ex=0.3, extend_angle=20, color=colorjam::rainbowJam(6))
#'
#' plot(NULL, xlim=c(-2, 8), ylim=c(1, 6), asp=1, xlab="", ylab="")
#' draw_twoway_contrast(
#' x0=c(1, 2, 1, 2, 1, 1, 0, -2, 4, 3, 2, 4),
#' x1=c(4, 5, 4, 5, 6, 6, 0, -2, 7, 6, 2, 4),
#' y0=c(1, 1.3, 2, 2.2, 4, 5, 5, 5, 3.2, 3, 6, 6),
#' y1=c(1, 1.3, 2, 2.2, 4, 5, 3, 3, 3.2, 3, 3.5, 3.5),
#' label=c("contrast one", "contrast two"), verbose=TRUE,
#' extend_ex=0.5, extend_angle=10,
#' color=colorjam::rainbowJam(12, Crange=c(90, 120)))
#'
#' draw_twoway_contrast(x0=c(4, 3), x1=c(4, 3), y0=c(2, 2), y1=c(1, 1),
#' label=c("contrast one", "contrast two"),
#' color=c("gold", "dodgerblue"), extend_angle=-20)
#' @export
draw_twoway_contrast <- function
(x0,
x1,
y0,
y1,
color="peachpuff",
border="black",
extend_ex=0.3,
extend_angle=10,
plot_type=c("base",
"grid"),
label=NULL,
label_sep="\n",
na.rm=TRUE,
label_color="white",
label_cex=1,
label_font=2,
oneway_position=0.5,
twoway_label=NULL,
twoway_label_color=label_color,
twoway_label_cex=label_cex,
twoway_label_font=label_font,
twoway_position=0.5,
twoway_lwd=5,
contingency=c(none="none",
half="scrunch",
full="loop"),
draw_oneway=TRUE,
drawing_order=c(
"two-two-one",
"one-two",
"two-one-two"),
do_plot=TRUE,
verbose=FALSE,
...)
{
# validate arguments
plot_type <- match.arg(plot_type);
contingency <- match.arg(contingency,
several.ok=TRUE);
contingency_names <- c("none", "half", "full");
if (!all(contingency_names %in% contingency)) {
contingency <- rep(contingency, length.out=3);
names(contingency) <- contingency_names;
}
drawing_order <- match.arg(drawing_order);
# ensure vectorized values are proper lengths
n <- max(c(length(x0), length(x1), length(y0), length(y1)));
if (n == 0) {
# consider adding a warning
return(NULL)
}
x0 <- rep(x0, length.out=n)
x1 <- rep(x1, length.out=n)
y0 <- rep(y0, length.out=n)
y1 <- rep(y1, length.out=n)
color <- rep(color, length.out=n);
colorset_twoway <- split(color, rep(seq_len(n / 2), each=2))
border <- rep(border, length.out=n);
# first draw the two one-way contrasts
if (TRUE %in% draw_oneway && "one-two" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
do_plot=do_plot,
verbose=verbose,
...)
}
# index values for first and second contrast
k1 <- seq(from=1, to=length(x0), by=2)
k2 <- k1 + 1;
# determine the two-way connector
contrast_angles <- jamba::rad2deg(atan2(y=(y1 - y0),
x=(x1 - x0)));
# flip each second contrast
contrast_angles[k2] <- (contrast_angles[k2] + 180) %% 360
# determine handedness of the two contrasts
hand <- point_handedness(
pt1=cbind(c(x0[k1]), c(y0[k1])),
pt2=cbind(c(x0[k2]), c(y0[k2])),
angle=contrast_angles[k1])
if (verbose) {
jamba::printDebug("draw_twoway_contrast(): ",
"hand: ", hand);
}
contrast_lengths <- sqrt(
(x1 - x0)^2 + (y1 - y0)^2)
# helper function to make bezier control points
make_bezier_lines_df <- function
(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex,
xadj,
yadj)
{
# Note: using length=1 instead of contrast_lengths[k1]
extend_ex <- rep(extend_ex, length.out=length(x0));
# so the extension has consistent length.
lines_df <- data.frame(
x=c(
# x0=x0[k1],
`x0.5`=(x0[k1] +
x1[k1])/2,
`x0.75`=(x0[k1] +
x1[k1]*3)/4,
x1=x1[k1],
`x1.2`=(x1[k1] +
xadj[k1] * 1 * extend_ex[k1]),
`x1.5`=(x1[k1] +
x0[k2])/2,
`x1.8`=(x0[k2] +
xadj[k2] * 1 * extend_ex[k2]),
x2=x0[k2],
`x2.25`=(x0[k2]*3 +
x1[k2])/4,
`x2.5`=(x0[k2] +
x1[k2])/2),
# x3=x1[k2]),
y=c(
# y0=y0[k1],
`y0.5`=(y0[k1] +
y0[k1])/2,
`y0.75`=(y0[k1] +
y0[k1]*3)/4,
y1=y1[k1],
`x1.2`=(y1[k1] +
yadj[k1] * 1 * extend_ex[k1]),
`y1.5`=(y1[k1] +
y0[k2])/2,
`y1.8`=(y0[k2] +
yadj[k2] * 1 * extend_ex[k2]),
y2=y0[k2],
`y2.25`=(y0[k2]*3 +
y1[k2])/4,
`y2.5`=(y0[k2] +
y1[k2])/2)
);
return(lines_df);
}
# determine appropriate angle
angle_diff <- -(extend_angle);
angle_diff <- ifelse(rep(hand, each=2) %in% "right",
extend_angle,
-extend_angle)
new_contrast_angles <- contrast_angles + angle_diff;
if (verbose) {
jamba::printDebug("draw_twoway_contrast(): ",
"new_contrast_angles: ");
print(data.frame(contrast_angles, hand=rep(hand, each=2),
angle_diff, new_contrast_angles));
}
# optionally mirror the angle when lines are too close?
# mirror the first contrast? might be useful when lines are too close
# new_contrast_angles[k1] <- (360 - new_contrast_angles[k1]) %% 360;
# mirror the second contrast? might be useful when lines are too close
# new_contrast_angles[k2] <- (360 - new_contrast_angles[k2]) %% 360;
# new_contrast_angles <- (360 - new_contrast_angles) %% 360;
# jamba::printDebug("new_contrast_angles:", new_contrast_angles); # debug
xadj <- cos(jamba::deg2rad(new_contrast_angles))
yadj <- sin(jamba::deg2rad(new_contrast_angles))
# define bezier control points for typical cases
lines_df <- make_bezier_lines_df(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex=extend_ex,
xadj, yadj);
# check for weird cases:
# - when control point x1.2 crosses either the
# x1.5 (midpoint) or
# x2.5 (opposite contrast)
# - test whether "handedness" changes relative to those points
x12_rows <- jamba::igrep("^x1.2", rownames(lines_df));
x15_rows <- jamba::igrep("^x1.5", rownames(lines_df));
x25_rows <- jamba::igrep("^x2.5", rownames(lines_df));
new_hand_25 <- point_handedness(
pt1=as.matrix(lines_df[x12_rows, , drop=FALSE]),
pt2=as.matrix(lines_df[x25_rows, , drop=FALSE]),
angle=contrast_angles[k1])
new_hand_15 <- point_handedness(
pt1=as.matrix(lines_df[x12_rows, , drop=FALSE]),
pt2=as.matrix(lines_df[x15_rows, , drop=FALSE]),
angle=contrast_angles[k1])
# if it crosses x25, we should loop
# if it crosses x15 but not x25, maybe we scrunch
changed_hands_25 <- (hand != new_hand_25);
changed_hands_15 <- (hand != new_hand_15);
## summarize the contingency scenario, defined as:
# none - the control point does not cross the halfieway
# half - the control point crosses the halfieway, not the other contrast
# full - the control point crosses the other contrast
contingency_scenario <- ifelse(
!changed_hands_25 & !changed_hands_15, "none",
ifelse(changed_hands_25, "full", "half"))
contingency_output <- contingency[contingency_scenario]
# calculate two-way contrast distance between component one-way contrasts
calc_twoway_distance <- function
(x0, x1, y0, y1)
{
# calculate two-way distance
if (length(x1) < 2) {
return(NULL)
}
x1 <- rep(x1, length.out=length(x0));
y0 <- rep(y0, length.out=length(x0));
y1 <- rep(y1, length.out=length(x0));
xym <- cbind(c(x0, x1), c(y0, y1));
rownames(xym) <- jamba::makeNames(
rep(c("A", "B"), each=length(x0)),
suffix="_con")
xyseq <- rep(seq_along(x0), each=2) + c(0, length(x0))
xym1 <- xym[xyseq, , drop=FALSE]
xym1_split <- split(rownames(xym1),
rep(seq_len(length(x0)/2), each=4));
twoway_distances <- sapply(xym1_split, function(irows){
dm <- as.matrix(dist(xym1[irows, , drop=FALSE]))
acols <- grepl("con1", colnames(dm));
max(c(0.5,
min(dm[!acols, acols, drop=FALSE], na.rm=TRUE)))
})
return(twoway_distances)
}
# if (any(c(changed_hands_25, changed_hands_15))) {
twoway_distances <- calc_twoway_distance(x0, x1, y0, y1)
if (any(c("scrunch", "loop") %in% contingency_output)) {
# mirror the second angle?
# if (any(changed_hands_25)) {
extend_ex <- rep(extend_ex, length.out=length(contrast_angles))
do_loop <- ("loop" %in% contingency_output);
if (any(do_loop)) {
k1_changed <- k1[do_loop];
k2_changed <- k2[do_loop];
# extend_ex[k1_changed] <- extend_ex[k1_changed] * 5;
# extend_ex[k1_changed] <- 2;
extend_ex[k1_changed] <- twoway_distances[do_loop] + sqrt(twoway_distances[do_loop])/2;
# extend_ex[k2_changed] <- extend_ex[k2_changed] * 2;
extend_ex[k2_changed] <- sqrt(twoway_distances[do_loop]);
# extend_ex[k2_changed] <- twoway_distances[do_loop] / 1;
new_contrast_angles[k2_changed] <- (contrast_angles[k2_changed] -
# angle_diff) %% 360
angle_diff * sqrt(twoway_distances[do_loop])) %% 360
# new_contrast_angles[k2_changed] <- (360 -
# new_contrast_angles[k2_changed]) %% 360;
new_contrast_angles[k1_changed] <- (contrast_angles[k1_changed] +
60 * sign(angle_diff)) %% 360
}
# if (any(changed_hands_15 & !changed_hands_25)) {
do_scrunch <- ("scrunch" %in% contingency_output)
if (any(do_scrunch)) {
k1_changed <- k1[do_scrunch];
k2_changed <- k2[do_scrunch];
new_contrast_angles[k1_changed] <- (contrast_angles[k1_changed] +
angle_diff / 3);
new_contrast_angles[k2_changed] <- (contrast_angles[k2_changed] +
angle_diff / 3);
}
xadj <- cos(jamba::deg2rad(new_contrast_angles))
yadj <- sin(jamba::deg2rad(new_contrast_angles))
# define bezier control points for typical cases
lines_df <- make_bezier_lines_df(x0, x1, y0, y1,
k1, k2,
contrast_lengths,
extend_ex=extend_ex,
xadj, yadj);
}
# optionally adjust x1.5,y1.5 to be midpoint between x1.2-x1.8 and y1.2-y1.8
x12_rows <- jamba::igrep("^x1.2", rownames(lines_df));
x15_rows <- jamba::igrep("^x1.5", rownames(lines_df));
x18_rows <- jamba::igrep("^x1.8", rownames(lines_df));
lines_df[x15_rows, "x"] <- (lines_df[x12_rows, "x"] + lines_df[x18_rows, "x"]) / 2;
lines_df[x15_rows, "y"] <- (lines_df[x12_rows, "y"] + lines_df[x18_rows, "y"]) / 2;
# bezier::bezier() is not vectorized, so iterate each set of control points
k_multiple <- (length(x0) / 2)
# iterate to calculate each bezier curve
bezier_curves <- lapply(seq_len(k_multiple), function(k){
k_seq <- seq(from=k, length.out=9, by=k_multiple)
use_lines_df <- lines_df[k_seq, , drop=FALSE]
# optionally display the control points with labels for debugging
if (FALSE) {
points(use_lines_df,
pch=21,
cex=4,
col="grey",
bg="white")
text(use_lines_df, rownames(lines_df), pch=21, cex=0.8)
}
# calculate bezier curve
bezier_points <- bezier::bezier(
t=seq(from=0, to=4, length.out=100),
p=as.matrix(use_lines_df), deg=2)
bezier_points
})
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
if ("one-two" %in% drawing_order) {
ik <- 25:76
} else {
ik <- 24:76;
}
bezier_line_use <- bezier_points[ik, , drop=FALSE];
lines(bezier_line_use,
lwd=twoway_lwd + 2,
col=border[k * 2 - 1]);
}
# optionally draw one-way contrasts here
if (TRUE %in% draw_oneway && "two-one-two" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
}
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
if ("one-two" %in% drawing_order) {
ik <- 23:77;
} else {
ik <- 23:77;
}
# render thinner line with colored segments
bezier_use <- bezier_points[ik, , drop=FALSE];
graphics::segments(
x0=head(bezier_use, -1)[,1],
x1=tail(bezier_use, -1)[,1],
y0=head(bezier_use, -1)[,2],
y1=tail(bezier_use, -1)[,2],
col=jamba::getColorRamp(
# c("dodgerblue", "firebrick2"),
colorset_twoway[[k]],
n=nrow(bezier_use) - 1),
lwd=twoway_lwd)
}
# optionally draw one-way contrasts here
if (TRUE %in% draw_oneway && "two-two-one" %in% drawing_order) {
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=color,
border=border,
plot_type=plot_type,
label=NULL,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
# optional "flourish" to re-draw the start/end
# iterate to draw two-way border lines for each connector
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# render wider line to display a border
ik <- 23:77;
# then take first 5, last 5 points
# render thinner line with colored segments
bezier_use <- bezier_points[ik, , drop=FALSE];
bezier_use_start <- head(bezier_use, 5);
bezier_use_end <- tail(bezier_use, 5);
bezier_colors <- jamba::getColorRamp(
colorset_twoway[[k]],
n=nrow(bezier_use) - 1);
graphics::segments(
x0=head(bezier_use_start, -1)[,1],
x1=tail(bezier_use_start, -1)[,1],
y0=head(bezier_use_start, -1)[,2],
y1=tail(bezier_use_start, -1)[,2],
col=head(bezier_colors, 5),
lwd=twoway_lwd)
graphics::segments(
x0=head(bezier_use_end, -1)[,1],
x1=tail(bezier_use_end, -1)[,1],
y0=head(bezier_use_end, -1)[,2],
y1=tail(bezier_use_end, -1)[,2],
col=tail(bezier_colors, 5),
lwd=twoway_lwd)
}
# last step is to draw labels so they are not covered by the bezier curve
# oneway labels
doc <- draw_oneway_contrast(
x0=x0,
x1=x1,
y0=y0,
y1=y1,
color=NA,
border=NA,
plot_type=plot_type,
label=label,
label_sep=label_sep,
na.rm=na.rm,
label_color=label_color,
label_cex=label_cex,
label_font=label_font,
oneway_position=oneway_position,
do_plot=do_plot,
verbose=verbose,
...)
# twoway labels
for (k in seq_along(bezier_curves)) {
bezier_points <- bezier_curves[[k]];
# define where to place the label
kn <- floor(twoway_position * 50) + 25;
# grab points in the middle
klen <- 7;
kn_start <- min(c(max(c(kn - klen, 15)), 85 - klen * 2))
ik <- seq(kn_start, length.out=15);
kn <- floor(mean(ik));
# ik <- 43:57;
bezier_use <- bezier_points[ik, , drop=FALSE];
# optionally render thinner line with colored segments
# graphics::segments(
# x0=head(bezier_use, -1)[,1],
# x1=tail(bezier_use, -1)[,1],
# y0=head(bezier_use, -1)[,2],
# y1=tail(bezier_use, -1)[,2],
# col="grey25",
# lwd=twoway_lwd * 2)
vector_angle <- jamba::rad2deg(atan2(
y=(tail(bezier_use, 1)[, 2] - head(bezier_use, 1)[, 2]),
x=(tail(bezier_use, 1)[, 1] - head(bezier_use, 1)[, 1]))) %% 360;
# discretize the angles so nearly parallel labels are
# likely to be parallel
# (most noticeable when one is 91 and the other is 89,
# and the labels are flipped left/right)
vector_angle <- round(vector_angle / 22.5) * 22.5;
# jamba::printDebug("vector_angle:", vector_angle);# debug
# round to integer values
twoway_label_angle <- round(
((vector_angle + 90) %% 180 - 90) %% 360);
use_angle_flip <- (twoway_label_angle != vector_angle)
use_adj <- c(
ifelse(use_angle_flip,
1 - (round(twoway_position * 8) / 8),
round(twoway_position * 8) / 8),
0.5);
jamba::shadowText(
x=bezier_points[kn, 1],
y=bezier_points[kn, 2],
col=twoway_label_color,
srt=twoway_label_angle,
cex=twoway_label_cex,
alphaOutline=getOption("jam.alphaOutline", 0.95),
r=getOption("jam.shadow.r", 0.1),
n=getOption("jam.shadow.n", 8),
# adj=c(0.5, 0.5),
adj=use_adj,
font=twoway_label_font,
jamba::cPaste(twoway_label, sep="\n"))
}
}
invisible(NULL)
}
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