1 ggplot2“银河系”

ggplot2等高线图版本的“银河系”

Published

August 12, 2025

在2025-07-29日，我们展示过H&E起源版本的“银河系”（QuPath：“银河系”起源于H&E），笔者在这里尝试通过R的ggplot2（包括代码/R codes）来展示该“银河系”。

1. 加载R包

# load packages
library(tidyverse) # Load the tidyverse package (include ggplot2) for data manipulation and visualization
library(RColorBrewer) # For color palettes

2. 读取表格数据并选择坐标列

# read the table containing the location of detected objects (i.e. nuclei)
txt_file <- "raw_data/2025-08-12_QuPath_InstanSeg.txt"
df <- txt_file |> read_delim(delim = "\t", col_names = TRUE, show_col_types = FALSE)

df |> names() # Display the column names

 [1] "Image"                 "Object ID"             "Object type"          
 [4] "Name"                  "Classification"        "Parent"               
 [7] "ROI"                   "Centroid X µm"         "Centroid Y µm"        
[10] "Area µm^2"             "Length µm"             "Circularity"          
[13] "Solidity"              "Max diameter µm"       "Min diameter µm"      
[16] "Hematoxylin: Mean"     "Hematoxylin: Median"   "Hematoxylin: Min"     
[19] "Hematoxylin: Max"      "Hematoxylin: Std.Dev." "Eosin: Mean"          
[22] "Eosin: Median"         "Eosin: Min"            "Eosin: Max"           
[25] "Eosin: Std.Dev."

df <- df |> select(`Centroid X µm`, `Centroid Y µm`) # Select the two columns which correspond to the X and Y coordinates of detected nuclei

df |> head() # Display the first six rows of the data frame

# A tibble: 6 × 2
  `Centroid X µm` `Centroid Y µm`
            <dbl>           <dbl>
1            131.            88.4
2            118.            90.2
3            169.            90.9
4            179.            95.0
5            230.            96.5
6            119.            96.8

3. 增加一个“random_color”列，用于每个细胞核颜色的随机分配

palette <- brewer.pal(8, "Set2") # get a color palette

df <- df |> 
  mutate(random_color = sample(palette, nrow(df), replace = TRUE)) # add a random color column

df |> head() # Display the first six rows of the updated data frame

# A tibble: 6 × 3
  `Centroid X µm` `Centroid Y µm` random_color
            <dbl>           <dbl> <chr>       
1            131.            88.4 #A6D854     
2            118.            90.2 #A6D854     
3            169.            90.9 #FC8D62     
4            179.            95.0 #E78AC3     
5            230.            96.5 #B3B3B3     
6            119.            96.8 #A6D854

4. 设定一个个性化的主题（theme）

# set a custome theme
custom_theme <- theme(
  panel.grid = element_blank(), # remove grid lines
  axis.text = element_blank(), # remove axis text
  axis.title = element_blank(), # remove axis titles
  axis.ticks = element_blank(), # remove axis ticks
  legend.position = "none", # remove legend
  panel.background = element_blank(), # remove panel background
  plot.background = element_blank(), # remove plot background
  plot.margin = margin(0, 0, 0, 0, "cm") # remove plot margins
)

5. 显示“银河系”对应的细胞核分布

ggplot(df, aes(x = `Centroid X µm`, y = `Centroid Y µm`)) +
  geom_point(aes(color = random_color)) + # scatter plot
  scale_x_continuous(limits = c(0, 896)) + # set x limits
  scale_y_continuous(limits = c(0, 768)) + # set y limits
  custom_theme # apply custom theme

6. 显示“银河系”对应的细胞核分布和等高线图

ggplot(df, aes(x = `Centroid X µm`, y = `Centroid Y µm`)) +
  geom_point(aes(color = random_color)) + # scatter plot
  geom_density_2d_filled(alpha = 0.6) + # add filled contour lines with transparency
  scale_fill_brewer(palette = "YlGn") + # set fill color palette
  scale_x_continuous(limits = c(0, 896)) + # set x limits
  scale_y_continuous(limits = c(0, 768)) + # set y limits
  custom_theme # apply custom theme

7. “银行系”的起源

给我买杯茶🍵