设置配色、图例和主题

本页目录

本页准备
从数据角色构建样式
固定样式和用户标度优先
组织可读图例
为场景选择主题
完成后检查

让颜色表达明确含义：先决定类别或连续数值，再选择映射、标度和图例。网站强调色不决定数据配色。

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)
  )
}

从数据角色构建样式

例子明确声明类别：区间连接填色映射 query ID，序列颜色映射序列 ID，基因填色映射链。手动标度的名称与实际取值匹配。

代码p_styled <- ggchord(seq_data = seqs, ribbon_data = links, gene_data = genes) +
  geom_seq() +
  geom_link_ribbon(aes(ribbon_fill = qaccver), alpha = .5) +
  geom_gene() +
  geom_seq_label(size = 4) +
  coord_collinear() +
  doc_axis() +
  scale_seq_colour_manual(values = seq_palette) +
  scale_gene_fill_manual(values = gene_palette) +
  scale_ribbon_fill_manual(values = seq_palette) +
  guides(gene_fill = guide_ggchord_legend(nrow = 1, theme = doc_legend_theme)) +
  doc_theme
theme_variants <- list(minimal = theme_ggchord_minimal(), dark = theme_ggchord_dark(), plasmid = theme_ggchord_plasmid())
p_styled

角色	映射数据	常用标度家族
`seq_colour`, `seq_ring`	序列/类别	序列颜色或 ring 手动标度
`ribbon_fill`, `ribbon_alpha`, `ribbon_colour`, `ribbon_linetype`	比对元数据或统计	手动、渐变/分段/identity 和透明度标度
`feature_fill`, `feature_shape`, `gene_fill`, `region_fill`	注释类别或链	相应角色的手动/预设标度
`link_colour`, `link_alpha`, `link_linewidth`, `link_linetype`	点连接元数据	连续或手动 link标度
`track_value`, `track_fill`, `track_colour`	命名轨道的数值/类别	命名数值域与颜色/填色标度

固定样式和用户标度优先

常量样式写在 aes() 外，变化样式写在映射中并配合合适的标度。显式几何层固定值优先，省略该固定参数才保持映射。用户标度优先于自动默认。同类多层独立保留数据、映射和参数。按 accver 命名的几何向量，不表示标度也接受逐序列列表。

组织可读图例

guide_ggchord_legend() 控制离散角色图例，guide_ggchord_colourbar() 控制连续颜色图例。colour/color 拼写别名保留，本文优先用 colour。图层 show.legend 决定显示，guides() 选择图例，theme(legend.position = ...) 决定位置。过宽图例可分行或增加导出宽度，不需要删减生物学数据来迁就。

为场景选择主题

例子在 theme_variants 中保存 minimal、dark 和 plasmid 备选，按场景添加到相应图中。上图使用 theme_ggchord_publication()，plasmid 预设用于圆图流程。主题控制非数据外观，不选择坐标系，也不替代数据驱动的填色标度。文字外观用 theme(text = element_text(...))；已删除的 base_size 式快捷参数见迁移指南。

完成后检查

同一 query 的连接颜色一致；连续相似度应使用连续标度。固定颜色放在 aes() 外，图例必须能说明映射。

继续：调整图形 →