生信基地圣诞树~
MERRY CHRISTMAS
写在前面
祝大家圣诞节快乐！Merry Christmas！愿大家在这冬日里邂逅所有美好与惊喜，科研顺利，文章多多~
圣诞节来临意味着2025年也快进入尾声，Biomamba 生信基地 在这一年里为大家呈现许多丰富的内容，其中包含三个全程班(R语言 scRNA-seq分析、Python scRNA-seq分析和Python 空间转录组分析)和2025年订阅资料。这里我主要展示我们手册和课程中使用到的工具，并绘制了三个圣诞树：2025订阅圣诞树 ，单细胞工具圣诞树、空转工具圣诞树，供大家学习和参考。（圣诞树代码：参考如何用R语言生成词云和Jodie Burchel的教程[1]）
------Biomamb
圣诞树展示
生信基地圣诞树，文末有大图~
2025订阅圣诞树的词条为：
《Cancer Cell》|时空单细胞揭示CRC的PD-1治疗免疫细胞动态
代码复现|吞噬作用增强肿瘤中巨噬细胞的氧化代谢和免疫抑制特征
肿瘤异质性分析必备| 一文学会四种scRNA-seq拷贝数变异分析
代码复现| scRNA-seq揭示人纤维化皮肤病中的成纤维细胞异质性与增殖
《NC》代码复现|snATAC联合scRNA-seq揭示小鼠肾脏细胞分化程序与疾病靶点
三种方法教你搞定空转数据邻域分析：squidpy+stSME+NMF分解
空转细胞通讯分析学习手册：CellPhoneDB+Commot+stLearn
《Nature Genetics》文献复写 | 结直肠癌免疫细胞的高清空转分析（Visium HD+Xeniu）
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单细胞圣诞树的词条为：
Python版本的是我们2026年的订阅合集，欢迎大家订阅和关注~
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空间转录组圣诞树的词条为：
向下滑动查看更多内容
圣诞树绘制代码
# 安装并加载必要的包
if (!require("ggplot2")) install.packages("ggplot2")
if (!require("ggwordcloud")) install.packages("ggwordcloud")
if (!require("dplyr")) install.packages("dplyr")
if (!require("cowplot")) install.packages("cowplot")
if (!require("grid")) install.packages("grid")
library(ggplot2)
library(ggwordcloud)
library(dplyr)
library(cowplot)
library(grid)
# 1. 定义您的词条（完整列表）
terms <- c(
换成上面的词条
)
# 创建词云数据框 - 竖排只需要每个词条一次
create_wordcloud_data <- function(terms) {
df <- data.frame(
word = terms,
freq = sapply(terms, function(x) {
base_freq <- 50 / sqrt(nchar(x)) # 基础频率
keywords <- c("scRNA", "空转", "空间", "单细胞", "复现", "分析", "手册")
keyword_bonus <- sum(sapply(keywords, function(kw) grepl(kw, x, fixed = TRUE))) * 8
return(round(base_freq + keyword_bonus))
})
)
return(df)
}
wordcloud_data <- create_wordcloud_data(terms)
# 2. 创建竖排词云图形 - 只有一列，缩小行间距，隐藏图例
create_vertical_wordcloud <- function(data) {
# 计算竖排位置
n <- nrow(data)
# 在圣诞树中心创建一列位置
# x坐标固定在一个位置，y坐标从上到下分布
# 缩小行间距：将y范围从18-5改为18-7，间距更小
x_pos <- rep(11, n) # 固定在中心位置x=11
y_pos <- seq(17.5, 6, length.out = n) # 从上到下分布，缩小行间距
# 创建数据框包含位置信息
data$x <- x_pos
data$y <- y_pos
# 创建竖排词云 - 保留颜色渐变但隐藏图例
p <- ggplot(data, aes(x = x, y = y, label = word, size = freq, color = freq)) +
geom_text(
hjust = 0.5, # 水平居中
vjust = 0.5, # 垂直居中
angle = 0, # 不旋转
alpha = 0.9, # 透明度
family = "STHeiti" # 中文字体，如果没有可以改为"sans"
) +
scale_size_area(max_size = 6, guide = "none") + # 隐藏字体大小图例
# 圣诞树配色：红色、金色、绿色、白色 - 保留渐变
scale_color_gradientn(
colors = c("#FF0000", "#FFD700", "#32CD32", "#FFFFFF"),
guide = "none" # 关键：隐藏颜色图例
) +
theme_void() +
theme(
plot.background = element_rect(fill = "transparent", color = NA),
panel.background = element_rect(fill = "transparent", color = NA),
plot.margin = margin(0, 0, 0, 0),
legend.position = "none" # 确保没有任何图例
) +
# 限制坐标范围到圣诞树绿色区域
xlim(5, 17) +
ylim(5, 18)
return(p)
}
# 3. 创建圣诞树图形（修正版）- 保持原样
create_christmas_tree <- function() {
# 圣诞树数据
Tree.X <- c(10, 11, 12, 10, 11, 12, 10, 11, 12, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 7, 8, 9, 10, 11, 12, 13, 14, 15, 7, 8, 9, 10, 11, 12, 13, 14, 15, 8, 9, 10, 11, 12, 13, 14, 8, 9, 10, 11, 12, 13, 14, 9, 10, 11, 12, 13, 10, 11, 12, 10, 11, 12, 11, 6, 7, 8, 6, 7, 8, 3, 4, 3, 4, 14, 15, 16, 14, 15, 16, 18, 19, 18, 19)
Tree.Y <- c(1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 16, 16, 16, 17, 17, 17, 18, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2)
Tree.Colour <- c(
rep("#143306", 148),
rep("blueviolet", 6),
rep("firebrick2", 10),
rep("blueviolet", 4)
)
ChristmasTree <- data.frame(Tree.X, Tree.Y, Tree.Colour)
tree <- ggplot() +
geom_tile(data = ChristmasTree, aes(x = Tree.X, y = Tree.Y, fill = Tree.Colour)) +
scale_fill_identity() +
theme_void() +
labs(x = "", y = "") +
theme(
plot.background = element_rect(fill = "black", color = NA),
plot.margin = margin(20, 20, 20, 20),
panel.background = element_rect(fill = "black", color = NA)
)
# 添加装饰灯光
set.seed(123)
Desired.Lights <- 50
Lights <- data.frame(
Lights.X = c(round(runif(round(Desired.Lights * 0.35), 4, 18), 0),
round(runif(round(Desired.Lights * 0.20), 5, 17), 0),
round(runif(round(Desired.Lights * 0.17), 6, 16), 0),
round(runif(round(Desired.Lights * 0.13), 7, 15), 0),
round(runif(round(Desired.Lights * 0.10), 8, 14), 0),
round(runif(round(Desired.Lights * 0.05), 10, 12), 0)),
Lights.Y = c(round(runif(round(Desired.Lights * 0.35), 4, 6), 0),
round(runif(round(Desired.Lights * 0.20), 7, 8), 0),
round(runif(round(Desired.Lights * 0.17), 9, 10), 0),
round(runif(round(Desired.Lights * 0.13), 11, 12), 0),
round(runif(round(Desired.Lights * 0.10), 13, 14), 0),
round(runif(round(Desired.Lights * 0.05), 15, 17), 0))
)
tree <- tree +
geom_point(data = Lights, aes(x = Lights.X, y = Lights.Y),
colour = "lightgoldenrodyellow", shape = 16, size = 2, alpha = 0.7)
# 添加装饰球
Baubles <- data.frame(
Bauble.X = c(6, 9, 15, 17, 5, 13, 16, 7, 10, 14, 7, 9, 11,
14, 8, 14, 9, 12, 11, 12, 14, 11, 17, 10),
Bauble.Y = c(4, 5, 4, 4, 5, 5, 5, 6, 6, 6, 8, 8, 8, 8, 10,
10, 11, 11, 12, 13, 10, 16, 7, 14),
Bauble.Colour = factor(c(1, 2, 2, 3, 2, 3, 1, 3, 1, 1, 1, 2, 1, 2,
3, 3, 2, 1, 3, 2, 1, 3, 3, 1)),
Bauble.Size = c(1, 3, 1, 1, 2, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3,
2, 3, 1, 1, 2, 2, 3, 3, 2)
)
tree <- tree +
geom_point(data = Baubles, aes(x = Bauble.X, y = Bauble.Y,
colour = Bauble.Colour, size = Bauble.Size),
shape = 16) +
scale_colour_manual(values = c("firebrick2", "gold", "dodgerblue3")) +
scale_size_area(max_size = 8) +
theme(legend.position = "none")
# 添加底座装饰
tree <- tree +
geom_segment(aes(x = 2.5, xend = 4.5, y = 1.5, yend = 1.5),
colour = "blueviolet", linewidth = 2) +
geom_segment(aes(x = 5.5, xend = 8.5, y = 1.5, yend = 1.5),
colour = "dodgerblue3", linewidth = 2) +
geom_segment(aes(x = 13.5, xend = 16.5, y = 1.5, yend = 1.5),
colour = "blueviolet", linewidth = 2) +
geom_segment(aes(x = 17.5, xend = 19.5, y = 1.5, yend = 1.5),
colour = "dodgerblue3", linewidth = 2) +
geom_segment(aes(x = 3.5, xend = 3.5, y = 0.5, yend = 2.5),
colour = "blueviolet", linewidth = 2) +
geom_segment(aes(x = 7.0, xend = 7.0, y = 0.5, yend = 2.5),
colour = "dodgerblue3", linewidth = 2) +
geom_segment(aes(x = 15.0, xend = 15.0, y = 0.5, yend = 2.5),
colour = "blueviolet", linewidth = 2) +
geom_segment(aes(x = 18.5, xend = 18.5, y = 0.5, yend = 2.5),
colour = "dodgerblue3", linewidth = 2)
# 添加树顶星星
tree <- tree +
annotate("text", x = 11, y = 19.5, label = "★",
size = 15, color = "gold", family = "serif")
# 添加标题
tree <- tree +
annotate("text", x = 11, y = 21.5,
label = "生物信息学知识树",
color = "white", size = 6, fontface = "bold")
return(tree)
}
# 4. 创建组合图形 - 调整叠加位置
create_combined_plot <- function() {
# 创建圣诞树
tree_plot <- create_christmas_tree()
# 创建竖排词云
wc_plot <- create_vertical_wordcloud(wordcloud_data)
# 使用cowplot组合图形
combined <- ggdraw() +
# 首先绘制圣诞树背景
draw_plot(tree_plot, x = 0, y = 0, width = 1, height = 1) +
# 然后在圣诞树上方叠加竖排词云
draw_plot(wc_plot,
x = 0.2, # 水平位置
y = 0.1, # 垂直位置
width = 0.65, # 宽度
height = 0.65) # 高度
return(combined)
}
# 5. 生成并显示组合图形
combined_plot <- create_combined_plot()
print(combined_plot)
# 6. 保存图片
ggsave("bioinfo_christmas_tree.png",
combined_plot,
width = 12,
height = 14,
dpi = 300,
bg = "black")输入不同的词条，可依次得到图片：
参考：
1\]https://zhuanlan.zhihu.com/p/449852173 MERRY CHRISTMAS **圣诞节快乐** MERRY CHRISTMAS圣节诞快乐 BEST WISHES美好祝福送给你  **圣诞快乐**