0.16.6 文档
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调整图形
把常见调整放到正确的 ggplot2 组件：数据映射、几何位置、坐标和主题各负其责。
本页准备
在新的 R 会话中先运行下方代码，再按页面顺序继续。配色和排版是可选的显示设置，输入只选择需要的列。
准备代码 · 在本页运行一次
代码
library(ggchord)
library(dplyr)
data(seq_data_example)
data(ribbon_data_example)
data(gene_data_example)
seqs <- seq_data_example |>
select(accver, length)
links <- ribbon_data_example |>
select(qaccver, saccver, qstart, qend, sstart, send)
# The fixture preserves biological strands separately from its old display strands.
genes <- gene_data_example |>
transmute(accver, start, end, strand = source_strand)
# Optional appearance choices; none of these columns or scales is required input.
library(ggchord)
seq_palette <- setNames(
c("#E64B35", "#233E4A", "#269B82", "#D59B17"),
c("MT108731.1", "MT118296.1", "OQ646790.1", "OR222515.1")
)
gene_palette <- c("+" = "#CE1536", "-" = "#346B9D", "." = "#8291A6")
library(ggchord)
doc_background <- "#FFFCF5"
identity_palette <- c("#303B71", "#36537D", "#269B82", "#A5D52C", "#ECEB31")
identity_values <- c(0, 0.5, 0.8, 0.9, 1)
identity_breaks <- c(0, 50, 80, 90, 100)
doc_legend_theme <- theme(
legend.title = element_text(size = 13, face = "bold"),
legend.text = element_text(size = 11),
legend.key.width = unit(9, "mm"), legend.key.height = unit(5, "mm"),
legend.spacing.x = unit(9, "mm"), legend.spacing.y = unit(7, "mm"),
legend.margin = margin(l = 4, r = 4, unit = "mm")
)
sequence_guide <- guide_ggchord_legend(nrow = 1, theme = doc_legend_theme)
strand_guide <- guide_ggchord_legend(
nrow = 1, override.aes = list(strand = c("+", "-")), theme = doc_legend_theme
)
identity_guide <- guide_ggchord_colourbar(
position = "left", direction = "vertical",
theme = theme(
legend.key.height = unit(75, "mm"), legend.key.width = unit(5, "mm"),
legend.title = element_text(size = 13, face = "bold"),
legend.text = element_text(size = 11), legend.margin = margin(r = 7, unit = "mm")
)
)
doc_theme <- theme_ggchord_publication(
axis.text = element_text(size = 11),
axis.text.check.overlap = TRUE
) +
theme(
legend.position = "bottom",
legend.title = element_text(size = 13, face = "bold"),
legend.text = element_text(size = 11),
legend.key.width = unit(9, "mm"), legend.key.height = unit(5, "mm"),
legend.spacing.x = unit(9, "mm"), legend.spacing.y = unit(7, "mm"),
legend.box.spacing = unit(6, "mm"),
plot.background = element_rect(fill = doc_background, colour = NA),
panel.background = element_blank(),
plot.title = element_text(face = "bold", size = 18),
plot.subtitle = element_text(size = 10, colour = "#5C625A"),
plot.margin = margin(14, 18, 14, 18)
)
doc_axis <- function(coordinates = "relative") {
scale_seq_position_continuous(
coordinates = coordinates, n.breaks = 3, minor_breaks = NULL,
labels = function(x) format(x, scientific = FALSE, big.mark = ",", trim = TRUE)
)
}职责分配
| 任务 | 接口 |
|---|---|
| 把数据列映射到 aesthetic | aes() |
| 定义映射规则与图例 |
scale_*(), guides()
|
| 几何与固定样式 | geom_*() |
| 局部放置 | position_*() |
| 全局坐标系 | coord_*() |
| 非数据外观 |
theme_*(), theme()
|
| 标题与说明 | labs() |
固定样式可直接传给几何层，数据驱动差异则使用映射和标度。显式固定值优先于映射， 省略固定参数则保留映射；用户标度优先于自动默认值。 shape 是固定注释几何参数，feature_shape 仍是映射角色。 显式 shape = NULL 无效，不表示改用映射。
映射连接相似度
代码
identity_links <- ribbon_data_example |>
select(qaccver, saccver, qstart, qend, sstart, send, pident)
p_mapped <- ggchord(seq_data = seqs, ribbon_data = identity_links) +
geom_seq() +
geom_link_ribbon(aes(ribbon_fill = pident), alpha = .6) +
scale_ribbon_fill_gradientn(
colours = identity_palette, values = identity_values,
limits = c(0, 100), breaks = identity_breaks, name = "Identity (%)", guide = identity_guide
) +
scale_seq_colour_manual(values = seq_palette) +
coord_chord(rotation = 20) +
labs(title = "Sequence comparison") +
doc_theme
p_mapped放置注释
使用 position_strand(c("+" = .1, "-" = -.2)) 指定带符号的逐链位移。 position_feature_stack() 处理重叠注释，position_track() 分配命名定量轨道。 逐序列几何参数可用单值、等长无名向量或按 accver 命名的向量；推荐命名向量。 这套语法不扩展到标度、图例或 theme。
每层独立拥有 data、mapping 和参数，同类注释/连接层不会互相替换。 show.legend 和 inherit.aes 遵循 ggplot2。输入角色映射在几何生成前处理， 后期视觉映射遵循 ggplot2 求值。详见 接口说明。
完成后检查
旋转整体图形使用 coord；逐序列几何使用明确命名值；颜色随数据变化时使用映射和标度。