2025-08-23_ggplot2版本的银河系-无细胞核面积的加权-vs-细胞核面积的加权.qmd

---
title: ggplot2“银河系”加权有无
subtitle: ggplot2版本的“银河系”：无细胞核面积的加权 vs. 细胞核面积的加权
date: 2025-08-23
toc-depth: 4
toc-expand: true
lang: en
---

在2025-07-29，我们展示过H&E起源版本的“银河系”（[QuPath：“银河系”起源于H&E](2025-07-29_银河系起源于HE.qmd)）。在2025-08-12，我们通过R的ggplot2来展示该“银河系”（[R：ggplot2等高线图版本的“银河系”](2025-08-12_ggplot2等高线图版本的银河系.qmd)）。在2025-08-15，我们进一步计算特定等高线的面积[R：ggplot2版本的“银河系”，并计算特定等高线的面积](2025-08-15_ggplot2版本的银河系-并计算特定等高线的面积.qmd)）。在2025-08-21，我们将等高线展示在原始H&E图片上（[R：ggplot2版本的“银河系”，并将等高线展示在H&E图上](2025-08-21_ggplot2版本的银河系-并将等高线展示在HE图上.qmd)）。

这次，我们通过ggplot2展示该“银河系”，且比较有无细胞核面积的加权。

## 1. Load packages and read data/加载包和读取数据

```{r}
#| message: false
#| warning: false
# load packages
library(tidyverse) # for data manipulation and visualization
library(RColorBrewer) # for color palettes
```

```{r}
# read the table
txt_file <- "raw_data/2025-08-12_QuPath_InstanSeg.txt" # specify the path to the text file
df <- txt_file |> read_delim(delim = "\t", col_names = TRUE, show_col_types = FALSE) # read the text file as a data frame
txt_file |> rm() # remove the txt_file variable to free up memory
```

```{r}
df <- df |> 
    dplyr::select(`Centroid X µm`, `Centroid Y µm`, `Area µm^2`) # select the columns specifying the coordinates and area of nuclei
df |> head() # display the first few rows of the data frame
```

## 2. 增加一个“random_color”列，用于每个细胞核颜色的随机分配

```{r}
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
```

## 3. Plot the nuclei as points and add contour lines/绘制无细胞核面积加权的分布图和有细胞核面积加权的分布图

### 3.1 Without weighted area/无细胞核面积加权

```{r}
nuclei_unweighted <- 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, 1000)) + # set x limits
  scale_y_continuous(limits = c(0, 900)) + # set y limits
  theme_classic() # apply classic theme

nuclei_unweighted

ggsave("images/2025-08-23_without-weighted-area.png", width = 8, height = 6, dpi = 300)
```

### 3.2 With weighted area/有细胞核面积加权

```{r}
nuclei_weighted <- ggplot(df, aes(x = `Centroid X µm`, y = `Centroid Y µm`)) +
  geom_point(aes(color = Random_color, size = `Area µm^2`), alpha = 1/2) + # scatter plot
  scale_size_area("Area\n(µm^2)", breaks = c(5, 10, 20, 40, 80, 120, 160)) + # set size scale
  scale_x_continuous(limits = c(0, 1000)) + # set x limits
  scale_y_continuous(limits = c(0, 900)) + # set y limits
  theme_classic() # apply classic theme

nuclei_weighted
```

## 4. “银河系”的起源

<img src="images/he_low.png" style="width: 100%; height: auto">

[给我买杯茶🍵](给我买杯茶.qmd)