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Merged
whelena merged 15 commits into from
May 15, 2026
+598 −340
Merged

Horizontal dendrogram and polygon plot #189

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5c688c6
add rotation to polygons
whelena Jan 15, 2026
4487c73
it's semi working, need to align xaxis and test with other plot types
whelena Jan 16, 2026
d9e1ac3
fix rotations to ensure plots remain centered in the viewplot
whelena May 8, 2026
fecad39
fix extend axis for both directions
whelena May 12, 2026
bc518c6
make axes flush against polygon
whelena May 12, 2026
0596db0
make sure no errors when yaxis is used
whelena May 13, 2026
4bc935e
make sure normal node is centered after padding in calculate.main.plo…
whelena May 13, 2026
e0ddbce
make text work in horizontal fishplot
whelena May 13, 2026
71cdfc1
fix axes label
whelena May 13, 2026
58edd15
clean up axis labels placing
whelena May 14, 2026
35922ef
Merge remote-tracking branch 'origin/main' into hwinata-horizontal-de…
whelena May 14, 2026
ab0e9ff
add gurdrails to iterative loops
whelena May 14, 2026
0855ceb
add script to update .Rda files for tests
whelena May 14, 2026
30e62d7
remove comments
whelena May 14, 2026
98f31a2
fix lintr
whelena May 15, 2026
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13 changes: 2 additions & 11 deletions R/SRCGrob.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,6 @@ SRCGrob <- function(
scale.size.2 = NA,
scale.padding = 1
) {
if ('CP' %in% colnames(tree) && !(plotting.direction %in% c('down', 0))) {
warning(paste(
'"plotting.direction" is not yet supported with "CP" polygon column.',
'"plotting.direction" will be ignored.'
));
}

if ('CCF' %in% colnames(tree) && !('CP' %in% colnames(tree))) {
tree$CP <- tree$CCF;
}

add.node.text <- !is.null(node.text);
add.polygons <- !is.null(tree$CP) && !disable.polygons;
Expand Down Expand Up @@ -137,7 +127,8 @@ SRCGrob <- function(
scale.bar.coords = scale.bar.coords,
scale.size.1 = scale.size.1,
scale.size.2 = scale.size.2,
scale.padding = scale.padding
scale.padding = scale.padding,
plotting.direction = plotting.direction
);

out.tree <- gTree(
Expand Down
5 changes: 2 additions & 3 deletions R/add.nodes.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ add.node.ellipse <- function(
node.radius,
label.nodes = NULL,
label.cex = NA,
add.normal = FALSE,
scale1,
...
) {
Expand Down Expand Up @@ -101,11 +100,11 @@ add.normal <- function(clone.out, node.radius, label.cex, normal.cex = 1) {
vp = vpStack(
make.plot.viewport(clone.out, clip = 'off'),
viewport(
y = unit(1, 'npc') - unit(node.radius * normal.cex, 'inches'),
y = unit(0, 'native'),
x = unit(0, 'native'),
height = grobHeight(normal.box),
width = grobWidth(normal.box),
just = c('centre', 'bottom')
just = c('centre', 'centre')
)
)
);
Expand Down
153 changes: 104 additions & 49 deletions R/add.text.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ axis.overlap <- function(
if (return.cex & !is.null(overlaps)) {
new.cex <- cex;

while (!is.null(overlaps)) {
while (!is.null(overlaps) && new.cex > 0.05) {
new.cex <- new.cex - 0.05;
overlaps <- axis.overlap(xpos, node.text, line.dist, axis.type, new.cex, panel.width);
}
Expand Down Expand Up @@ -119,9 +119,12 @@ position.node.text <- function(
split = FALSE,
label.nodes = FALSE,
adjust.axis.overlap = TRUE,
cex = cex
cex = cex,
plotting.direction = 'down'
) {

is.horizontal <- !is.numeric(plotting.direction) && plotting.direction %in% c('left', 'right');

text.grob.list <- vector('list', length(unlist(node.list)));
orig.cex <- cex;
idx <- 1;
Expand Down Expand Up @@ -191,6 +194,10 @@ position.node.text <- function(
(!label.nodes && (label.bottom + str.heightsum) > (tree.max.adjusted$y0[s] + node.radius * 0.5))
) {
cex <- cex - 0.05;
if (cex < 0.01) {
cex <- 0.01;
break;
}
}
}

Expand All @@ -209,10 +216,9 @@ position.node.text <- function(
vjust <- 'center';
} else {
ypos <- label.bottom + (g - 1) * spacing + heights - spacing;

#back computing the x position based on the intercept and the slope
xpos <- ifelse(
is.infinite(slope),
is.infinite(slope) || is.horizontal,
yes = tree.max.adjusted$x1[s],
no = (ypos - intercept) / slope
);
Expand All @@ -235,14 +241,24 @@ position.node.text <- function(
no = sum(str.heights.left[c(1:(g - 1))])
);

ypos <- label.bottom + (g - 1) * spacing + heights - spacing;
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos - xline.dist, 'inches'),
y = unit(ypos,'inches'),
just = c('right', 'bottom'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
if (is.horizontal) {
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(ypos, 'inches'),
y = unit(xpos - xline.dist, 'inches'),
just = c('right', 'top'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
} else {
ypos <- label.bottom + (g - 1) * spacing + heights - spacing;
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos - xline.dist, 'inches'),
y = unit(ypos,'inches'),
just = c('right', 'bottom'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
}
} else {
offset.left <- ceiling(length(node.text.col[[s]]) / 2);
heights <- ifelse((
Expand All @@ -251,15 +267,24 @@ position.node.text <- function(
no = sum(str.heights.right[c(1:(g - offset.left - 1))])
);

ypos <- label.bottom + (g - offset.left - 1) * spacing + heights - spacing;

text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist, 'inches'),
y = unit(ypos, 'inches'),
just = c('left', 'bottom'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
if (is.horizontal) {
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos, 'inches'),
y = unit(ypos + xline.dist, 'inches'),
just = c('right', 'bottom'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
} else {
ypos <- label.bottom + (g - offset.left - 1) * spacing + heights - spacing;
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist, 'inches'),
y = unit(ypos, 'inches'),
just = c('left', 'bottom'),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
}
}
} else if (alternating) {
# Alternate between placing the text to the left and to the right of the node
Expand All @@ -271,15 +296,25 @@ position.node.text <- function(
xline.dist.adj <- xline.dist;
}

text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist.adj, 'inches'),
y = unit(ypos, 'inches'),
just = just,
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
if (is.horizontal) {
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos, 'inches'),
y = unit(ypos + xline.dist.adj, 'inches'),
just = c('center', ifelse(xline.dist.adj > 0, 'bottom', 'top')),
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
} else {
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist.adj, 'inches'),
y = unit(ypos, 'inches'),
just = just,
gp = gpar(col = node.text.col[[s]][g], cex = cex)
);
}

if (adjust.axis.overlap) {
if (adjust.axis.overlap && !is.horizontal) {
overlaps.axis <- axis.overlap(
xpos, node.list[[s]][g],
xline.dist.adj,
Expand All @@ -304,7 +339,8 @@ position.node.text <- function(
node.radius = node.radius,
alternating = alternating,
split = split,
label.nodes = label.nodes
label.nodes = label.nodes,
plotting.direction = plotting.direction
);

return(text.grob.list);
Expand Down Expand Up @@ -418,7 +454,7 @@ position.node.text <- function(
}
}

if (adjust.axis.overlap) {
if (adjust.axis.overlap && !is.horizontal) {
overlaps.axis <- axis.overlap(
xpos,
node.list[[s]][g],
Expand All @@ -428,8 +464,10 @@ position.node.text <- function(
return.cex = TRUE
);

# Shrink the text if they overlap
if (!is.null(overlaps.axis)) {
# Shrink the text if they overlap; only recurse when
# axis.overlap found a strictly smaller cex, otherwise
# we would loop infinitely at the minimum cex value.
if (!is.null(overlaps.axis) && overlaps.axis < cex) {
text.grob.list <- position.node.text(
tree.max.adjusted = tree.max.adjusted,
node.list = node.list,
Expand All @@ -444,25 +482,42 @@ position.node.text <- function(
node.radius = node.radius,
alternating = alternating,
split = split,
label.nodes = label.nodes
label.nodes = label.nodes,
plotting.direction = plotting.direction
);

return(text.grob.list);
}
}
}

text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist, 'inches'),
y = unit(ypos, 'inches'),
just = c(hjust, vjust),
gp = gpar(
col = node.text.col[[s]][g],
fontface = node.text.fontface[[s]][g],
cex = cex
)
);
if (is.horizontal) {
offset.x <- ceiling(length(node.text.col[[s]]) / 2);
xpos <- tree.max.adjusted$x1[s] - ((tree.max.adjusted$x1[s] - tree.max.adjusted$x0[s]) * 0.5);
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos, 'inches'),
y = unit(ypos + xline.dist, 'inches'),
just = c('center', ifelse(xline.dist > 0, 'bottom', 'top')),
gp = gpar(
col = node.text.col[[s]][g],
fontface = node.text.fontface[[s]][g],
cex = cex
)
);
} else {
text.grob.list[[idx]] <- textGrob(
node.list[[s]][g],
x = unit(xpos + xline.dist, 'inches'),
y = unit(ypos, 'inches'),
just = c(hjust, vjust),
gp = gpar(
col = node.text.col[[s]][g],
fontface = node.text.fontface[[s]][g],
cex = cex
)
);
}
}

idx <- idx + 1;
Expand Down Expand Up @@ -490,13 +545,13 @@ add.text2 <- function(
node.radius = NULL,
alternating = TRUE,
split = TRUE,
clone.out = NULL
clone.out = NULL,
plotting.direction = 'down'
) {

# Radius in native units
node.radius <- node.radius / scale;
node.text <- node.text[node.text$node %in% tree$tip, ];

node.list <- vector('list', nrow(tree));
node.text.col <- vector('list', nrow(tree));
node.text.fontface <- vector('list', nrow(tree));
Expand Down Expand Up @@ -591,7 +646,6 @@ add.text2 <- function(

tree.max.adjusted$slope <- (tree.max.adjusted$y1 - tree.max.adjusted$y0) / (tree.max.adjusted$x1 - tree.max.adjusted$x0);
tree.max.adjusted$intercept <- tree.max.adjusted$y1 - tree.max.adjusted$slope * tree.max.adjusted$x1;

text.grob.list <- position.node.text(
tree.max.adjusted = tree.max.adjusted,
node.list = node.list,
Expand All @@ -606,7 +660,8 @@ add.text2 <- function(
node.radius = node.radius,
alternating = alternating,
split = split,
label.nodes = label.nodes
label.nodes = label.nodes,
plotting.direction = plotting.direction
);

text.grob.gList <- do.call(gList, text.grob.list);
Expand Down
2 changes: 1 addition & 1 deletion R/calculate.clone.polygons.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ make.polygon <- function(
vaf <- wid;

beta <- len / beta.in;
y1 <- max(y0 + beta, y0 + 1);
y1 <- y0 + beta #max(y0 + beta, y0 + 1);
yy <- seq(y0, y1, length.out = 100);

params.d <- c(-0.7310133, sig.shape);
Expand Down
39 changes: 36 additions & 3 deletions R/make.clone.tree.grobs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ make.clone.tree.grobs <- function(
scale.size.1,
scale.size.2,
scale.padding,
plotting.direction = 'down',
...
) {
#initializing dataframe for subclones
Expand Down Expand Up @@ -110,12 +111,42 @@ make.clone.tree.grobs <- function(
);

clone.out$no.ccf <- no.ccf;

# Rotate node positions and branch angles for fish plots (with CP data) when start.angle is non-zero
# This ensures branches and nodes rotate along with the polygons
if (!no.ccf && start.angle != 0) {
rotated.nodes <- rotate.coords(
x = clone.out$v$x,
y = clone.out$v$y,
rotate.by = start.angle,
x.origin = 0,
y.origin = 0
);
clone.out$v$x <- rotated.nodes$x;
clone.out$v$y <- rotated.nodes$y;

clone.out$tree$angle <- clone.out$tree$angle + start.angle;

for (j in seq_along(clone.out$clones)) {
rot.poly <- rotate.coords(
x = clone.out$clones[[j]]$x,
y = clone.out$clones[[j]]$y,
rotate.by = start.angle,
x.origin = 0,
y.origin = 0
);
clone.out$clones[[j]]$x <- rot.poly$x;
clone.out$clones[[j]]$y <- rot.poly$y;
}
}

plot.size <- calculate.main.plot.size(
clone.out,
scale1,
wid,
min.width,
node.radius
node.radius,
start.angle = start.angle
);

if (!no.ccf) {
Expand Down Expand Up @@ -159,7 +190,8 @@ make.clone.tree.grobs <- function(
no.ccf = no.ccf,
xaxis.label = xaxis.label,
yaxis1.label = yaxis1.label,
yaxis2.label = yaxis2.label
yaxis2.label = yaxis2.label,
plotting.direction = plotting.direction
);

if (scale.bar) {
Expand Down Expand Up @@ -200,7 +232,8 @@ make.clone.tree.grobs <- function(
node.radius = node.radius,
scale = scale1,
clone.out = clone.out,
alternating = FALSE
alternating = FALSE,
plotting.direction = plotting.direction
);

clone.out$grobs <- c(clone.out$grobs, list(node.text.grobs));
Expand Down
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