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Superseded: Add optional venny StatPlot backend #13

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7 changes: 4 additions & 3 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Type: Package
Package: thisplot
Title: Utility Functions for Plotting
Version: 0.3.8
Date: 2026-04-23
Version: 0.3.10
Date: 2026-05-28
Authors@R:
c(
person("Meng", "Xu", email = "mengxu98@qq.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8300-1054")),
Expand Down Expand Up @@ -50,7 +50,8 @@ Suggests:
scales,
stringr,
testthat (>= 3.0.0),
tidyr
tidyr,
venny
Config/Needs/website: mengxu98/thistemplate
Config/testthat/edition: 3
Encoding: UTF-8
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4 changes: 3 additions & 1 deletion NEWS.md
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@@ -1,12 +1,14 @@
# thisplot 0.3.9
# thisplot 0.3.10

* **feat**:
* `DimDataPlot()`: New lightweight helper for plotting supplied 2D coordinates from data frames, with grouping, splitting, shape mapping, labels, palettes, theme controls, and optional group marks.
* `StatPlot()`: Added configurable major panel grid lines via `grid_major`, `grid_major_colour`, `grid_major_linetype`, and `grid_major_linewidth`.
* `StatPlot()`: Added optional `venn_engine = "venny"` support for more flexible 2-4 set Venn diagrams while keeping `ggVennDiagram` as the default.

* **docs**:
* Added documentation and examples for `DimDataPlot()`.
* Updated `StatPlot()` documentation for the new major grid controls.
* Added `StatPlot()` documentation and examples for the optional `venny` Venn backend.

# thisplot 0.3.8

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274 changes: 181 additions & 93 deletions R/StatPlot.R
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Expand Up @@ -24,6 +24,14 @@
#' Can be one of `"bar"`, `"rose"`, `"ring"`, `"pie"`, `"trend"`,
#' `"trend_alluvial"`, `"area"`, `"dot"`, `"sankey"`, `"chord"`,
#' `"venn"`, or `"upset"`.
#' @param venn_engine The engine used when `plot_type = "venn"`.
#' Can be one of `"ggVennDiagram"` or `"venny"`.
#' Default is `"ggVennDiagram"`.
#' The `"venny"` engine supports 2 to 4 sets.
#' @param venn_args A list of additional arguments passed to
#' [venny::venny()] when `plot_type = "venn"` and
#' `venn_engine = "venny"`.
#' The `data` argument is generated internally and cannot be supplied here.
#' @param stat_type The type of statistic to compute for the plot.
#' Can be one of `"percent"` or `"count"`.
#' @param position The position adjustment for the plot.
Expand Down Expand Up @@ -164,6 +172,18 @@
#' group.by = "Group",
#' plot_type = "trend_alluvial"
#' )
#'
#' meta_data$A <- meta_data$Type == "A"
#' meta_data$B <- meta_data$Group == "X"
#' meta_data$C <- meta_data$Batch == "B1"
#' StatPlot(
#' meta_data,
#' stat.by = c("A", "B", "C"),
#' stat_level = TRUE,
#' plot_type = "venn",
#' venn_engine = "venny",
#' venn_args = list(detail = TRUE)
#' )
StatPlot <- function(
meta.data,
stat.by,
Expand All @@ -190,6 +210,8 @@ StatPlot <- function(
"venn",
"upset"
),
venn_engine = c("ggVennDiagram", "venny"),
venn_args = list(),
stat_type = c("percent", "count"),
position = c("stack", "dodge"),
palette = "Chinese",
Expand Down Expand Up @@ -227,7 +249,9 @@ StatPlot <- function(

stat_type <- match.arg(stat_type)
plot_type <- match.arg(plot_type)
venn_engine <- match.arg(venn_engine)
position <- match.arg(position)
venn_args <- venn_args %||% list()

if (identical(plot_type, "trend_alluvial")) {
check_r("ggalluvial", verbose = FALSE)
Expand Down Expand Up @@ -343,6 +367,27 @@ StatPlot <- function(
)
}
}
if (identical(plot_type, "venn") && identical(venn_engine, "venny")) {
if (!is.list(venn_args)) {
log_message(
"{.arg venn_args} must be a list",
message_type = "error"
)
}
if ("data" %in% names(venn_args)) {
log_message(
"{.arg venn_args} cannot contain {.arg data}; it is generated internally",
message_type = "error"
)
}
if (length(stat.by) < 2 || length(stat.by) > 4) {
log_message(
"{.arg stat.by} must contain 2 to 4 sets when {.arg venn_engine = 'venny'}",
message_type = "error"
)
}
check_r("venny", verbose = FALSE)
}

levels <- unique(
unlist(
Expand Down Expand Up @@ -982,6 +1027,7 @@ StatPlot <- function(
colors <- palette_colors(stat.by, palette = palette, palcolor = palcolor)
nlev <- nlevels(dat_all[[split.by]])
chord_use_temp <- plot_type == "chord" && isTRUE(combine) && nlev > 1L
venny_details <- list()
if (plot_type == "chord" && isTRUE(combine)) {
if (chord_use_temp) {
temp <- tempfile(fileext = "png")
Expand Down Expand Up @@ -1019,101 +1065,136 @@ StatPlot <- function(
cellkeep
}
)
venn <- ggVennDiagram::Venn(dat_list)
data <- ggVennDiagram::process_data(venn)
dat_venn_region <- ggVennDiagram::venn_region(data)
idname <- dat_venn_region[["name"]][
dat_venn_region[["name"]] %in% stat.by
]
names(idname) <- dat_venn_region[["id"]][
dat_venn_region[["name"]] %in% stat.by
]
idcomb <- strsplit(dat_venn_region[["id"]], split = "")
colorcomb <- lapply(idcomb, function(x) colors[idname[as.character(x)]])
dat_venn_region[["colors"]] <- sapply(
colorcomb,
function(x) blendcolors(x, mode = "blend")
)
dat_venn_region[["label"]] <- paste0(
dat_venn_region[["count"]],
"\n",
round(
dat_venn_region[["count"]] / sum(dat_venn_region[["count"]]) * 100,
1
),
"%"
)
dat_venn_setedge <- ggVennDiagram::venn_setedge(data)
dat_venn_setedge[["colors"]] <- colors[stat.by[as.numeric(
dat_venn_setedge[["id"]]
)]]

venn_regionedge_data <- ggVennDiagram::venn_regionedge(data)
venn_regionedge_data[["colors"]] <- dat_venn_region[["colors"]][match(
venn_regionedge_data[["id"]],
dat_venn_region[["id"]]
)]

p <- ggplot() +
geom_polygon(
data = venn_regionedge_data,
aes(X, Y, fill = colors, group = id),
alpha = alpha
) +
geom_path(
data = dat_venn_setedge,
aes(X, Y, group = id),
color = "black",
linewidth = 1,
show.legend = FALSE
) +
ggrepel::geom_text_repel(
data = ggVennDiagram::venn_setlabel(data),
aes(
X,
Y,
label = paste0(
name,
"\n(",
count,
")"
)
if (identical(venn_engine, "venny")) {
venny_result <- do.call(
venny::venny,
c(list(data = dat_list), venn_args)
)
venny_detail <- NULL
if (
is.list(venny_result) &&
!inherits(venny_result, c("gg", "ggplot")) &&
!is.null(venny_result[["venn"]])
) {
venny_detail <- venny_result
p <- venny_result[["venn"]]
} else {
p <- venny_result
}
if (!inherits(p, c("gg", "ggplot"))) {
log_message(
"{.fun venny::venny} must return a ggplot object or a list containing {.arg venn}",
message_type = "error"
)
}
p <- p + labs(x = sp, title = title, subtitle = subtitle)
if (!is.null(venny_detail)) {
attr(p, "venny_detail") <- venny_detail
venny_details[[sp]] <- venny_detail
}
} else {
venn <- ggVennDiagram::Venn(dat_list)
data <- ggVennDiagram::process_data(venn)
dat_venn_region <- ggVennDiagram::venn_region(data)
idname <- dat_venn_region[["name"]][
dat_venn_region[["name"]] %in% stat.by
]
names(idname) <- dat_venn_region[["id"]][
dat_venn_region[["name"]] %in% stat.by
]
idcomb <- strsplit(dat_venn_region[["id"]], split = "")
colorcomb <- lapply(
idcomb,
function(x) colors[idname[as.character(x)]]
)
dat_venn_region[["colors"]] <- sapply(
colorcomb,
function(x) blendcolors(x, mode = "blend")
)
dat_venn_region[["label"]] <- paste0(
dat_venn_region[["count"]],
"\n",
round(
dat_venn_region[["count"]] /
sum(dat_venn_region[["count"]]) * 100,
1
),
fontface = "bold",
colour = label.fg,
size = label.size + 0.5,
bg.color = label.bg,
bg.r = label.bg.r,
point.size = NA,
max.overlaps = 100,
force = 0,
min.segment.length = 0,
segment.colour = "black"
) +
ggrepel::geom_text_repel(
data = ggVennDiagram::venn_regionlabel(data),
aes(X, Y, label = count),
colour = label.fg,
size = label.size,
bg.color = label.bg,
bg.r = label.bg.r,
point.size = NA,
max.overlaps = 100,
force = 0,
min.segment.length = 0,
segment.colour = "black"
) +
scale_fill_identity() +
coord_fixed(ratio = 1, clip = "off") +
theme(
plot.title = element_text(hjust = 0.5),
plot.background = element_blank(),
panel.background = element_blank(),
axis.title.y = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank()
"%"
)
p <- p + labs(x = sp, title = title, subtitle = subtitle)
dat_venn_setedge <- ggVennDiagram::venn_setedge(data)
dat_venn_setedge[["colors"]] <- colors[stat.by[as.numeric(
dat_venn_setedge[["id"]]
)]]

venn_regionedge_data <- ggVennDiagram::venn_regionedge(data)
venn_regionedge_data[["colors"]] <- dat_venn_region[["colors"]][
match(
venn_regionedge_data[["id"]],
dat_venn_region[["id"]]
)
]

p <- ggplot() +
geom_polygon(
data = venn_regionedge_data,
aes(X, Y, fill = colors, group = id),
alpha = alpha
) +
geom_path(
data = dat_venn_setedge,
aes(X, Y, group = id),
color = "black",
linewidth = 1,
show.legend = FALSE
) +
ggrepel::geom_text_repel(
data = ggVennDiagram::venn_setlabel(data),
aes(
X,
Y,
label = paste0(
name,
"\n(",
count,
")"
)
),
fontface = "bold",
colour = label.fg,
size = label.size + 0.5,
bg.color = label.bg,
bg.r = label.bg.r,
point.size = NA,
max.overlaps = 100,
force = 0,
min.segment.length = 0,
segment.colour = "black"
) +
ggrepel::geom_text_repel(
data = ggVennDiagram::venn_regionlabel(data),
aes(X, Y, label = count),
colour = label.fg,
size = label.size,
bg.color = label.bg,
bg.r = label.bg.r,
point.size = NA,
max.overlaps = 100,
force = 0,
min.segment.length = 0,
segment.colour = "black"
) +
scale_fill_identity() +
coord_fixed(ratio = 1, clip = "off") +
theme(
plot.title = element_text(hjust = 0.5),
plot.background = element_blank(),
panel.background = element_blank(),
axis.title.y = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank()
)
p <- p + labs(x = sp, title = title, subtitle = subtitle)
}
}

if (plot_type == "upset") {
Expand Down Expand Up @@ -1329,6 +1410,13 @@ StatPlot <- function(
ncol = ncol,
byrow = byrow
)
if (
identical(plot_type, "venn") &&
identical(venn_engine, "venny") &&
length(venny_details) > 0
) {
attr(plot, "venny_detail") <- venny_details
}
} else {
plot <- plist[[1]]
}
Expand Down
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