particle_area_count_analysis/stress_granule_data_visualization.Rmd at main · BackusLab/particle_area_count_analysis · GitHub

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---
title: "AAV-SHKBP1 Analysis"
author: "Lucia Liu"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(ggplot2)
```


```{r}
# Input your csv pathname below
df <- read.csv('/Users/lucialiu/Downloads/2025.12.16 Ctrl-SHKBP1 DDC diet 2wks p62/czi/40x/Ctrl-SHKBP1 Final Output/Analysis Results/Ctrl_SHKBP1_summary.csv')
df_chow <- df %>% slice(1:10)
df_ddc <- df %>% slice(11:21)
```

```{r}
dark_blue <- "#12436D"
teal <- "#28A197"
orange <- "#F46A25"
lavender <- "#A285D1"
dark_red <- "#801650"
light_blue <- "#6BACE6"
medium_blue <- "#2073BC"
```

``` {r}
plot_bar_chart <- function(df, y_var, fill_color, y_label, title_label) {
  ggplot(data = df, aes(x=Slice, y={{ y_var }})) +
    geom_bar(stat = "identity", fill = fill_color) +
    theme(plot.title = element_text(hjust = 0.5),
          axis.text.x = element_text(angle = 45, hjust = 1)) +
    labs(x = 'Slice',
         y = y_label,
         title = title_label) +
    geom_text(aes(label={{ y_var }}), vjust=-0.75, size=2.5)
}
```

``` {r}
plot_bar_chart(df_chow, Area.of.C1...Area.of.C2, dark_blue,
               'Total Area of C1 / Total Area of C2',
               'Distribution of Ratio of Total Area of Chow Mice')
plot_bar_chart(df_chow, Area.of.Particles..C1....Cell, dark_blue,
               'Area of Particles Per Cell',
               'Distribution of Area of Particles Per Cell of Chow Mice')
```

``` {r}
plot_bar_chart(df_ddc, Area.of.C1...Area.of.C2, medium_blue,
               'Total Area of C1 / Total Area of C2',
               'Distribution of Ratio of Total Area of DDC Mice')
plot_bar_chart(df_ddc, Area.of.Particles..C1....Cell, medium_blue,
               'Area of Particles Per Cell',
               'Distribution of Area of Particles Per Cell of DDC Mice')
```

``` {r}
plot_combined_bar_chart <- function(y_var, label_size, y_label, title_label) {
  ggplot(data = df, aes(x=Slice, y={{ y_var }}, fill=Diet)) +
    geom_bar(stat = "identity") +
    theme(plot.title = element_text(hjust = 0.5),
          axis.text.x = element_text(angle = 45, hjust = 1)) +
    scale_fill_manual(values = c("Chow" = dark_blue, "DDC" = medium_blue)) +
    labs(x = 'Slice',
         y = y_label,
         title = title_label) +
    geom_text(aes(label={{ y_var }}), vjust=-0.75, size=label_size)
}
```

``` {r fig.width=8, dpi=300}
save_graph <- function(plot_name, filename) {
  ggsave(filename = paste0(filename, ".pdf"), plot = plot_name, device = "pdf", width = 7, height = 4.5, dpi = 350, units = "in")
  ggsave(filename = paste0(filename, ".svg"), plot = plot_name, device = "svg",width = 7, height = 4.5, units = "in")
}
```

``` {r fig.width=8, dpi=300}
total_area_graph <- plot_combined_bar_chart(Total.Area.C1, 1.5,
                        'Total Area of Particles (µm^2)',
                        'Distribution of Total Area of Particles')
save_graph(total_area_graph, 'total_area_distribution')
total_area_graph

area_per_cell_graph <- plot_combined_bar_chart(Area.of.Particles..C1....Cell, 1.8,
                        'Area of Particles Per Cell',
                        'Distribution of Area of Particles Per Cell')
save_graph(area_per_cell_graph, 'area_per_cell')
area_per_cell_graph

area_ratio_graph <- plot_combined_bar_chart(Area.of.C1...Area.of.C2, 1.8,
                        'Total Area of C1 / Total Area of C2',
                        'Distribution of Ratio of Total Area')
save_graph(area_ratio_graph, 'area_ratio')
area_ratio_graph

avg_particle_size_graph <- plot_combined_bar_chart(Avg.Particle.Size, 2,
                          'Average Particle Size (µm^2)',
                          'Distribution of Average Particle Size')
save_graph(avg_particle_size_graph, 'avg_particle_size')
avg_particle_size_graph
```

``` {r}
summary(df_chow$Total.Area.C1)
summary(df_ddc$Total.Area.C1)

summary(df_chow$Avg.Particle.Size)
summary(df_ddc$Avg.Particle.Size)

summary(df_chow$Area.of.Particles..C1....Cell)
summary(df_ddc$Area.of.Particles..C1....Cell)

summary(df_chow$Area.of.C1...Area.of.C2)
summary(df_ddc$Area.of.C1...Area.of.C2)
```