Cal_Explore.qmd

---
title: "Cal_Explore"
format: html
editor: visual
---

## Load Data

```{r}
#| warning: false
#| echo: false
#| include: false

library(tidyverse)
library(lubridate)
library(ggnewscale)

# Load .Rda from file browser
fpath <- file.choose()
load(fpath)

# Get file name from path 
tmp <- unlist(strsplit(fpath,"[\\]"))
filename <- tmp[length(tmp)]
print(paste('Data successfully loaded from',filename))

# Get file directory from path
repo <- paste0(tmp[1:length(tmp)-1],collapse="/")
repo <- paste0(repo,"/")

# Load Cal_Units.csv file
unitkeys <- read_csv(paste0(repo,'Cal_Units.csv'))
```

## Set visualization parameters

```{r}
#| warning: false
#| echo: false
#| include: false

# Specify grouping and faceting variables, color palette
# For color options see http://sape.inf.usi.ch/quick-reference/ggplot2/colour

df2plt      <- df.hourly # which binned data you want to vis
var         <- "EE" # which variable to plot - use colnames(df2plt)
groupvar    <- "Treatment"
facetvar    <- NA # set to NA (no quotes!) if no faceting desired
plt         <- "Dark2"
by_group    <- F # T for mean + SEM, F for individual subjects

# Defaults:
#circadian   <- T # get LD shading information automatically
```

#### Create plotting functions

```{r}
tsplot <- function(data,var,groupvar,facetvar,ylab) {
  ts <- data
  plot <- ggplot() +
  # Conditionally facet if facetvar is not NA
  {if(!is.na(facetvar) & facetvar %in% colnames(data))facet_grid(~ .data[[facetvar]])} +  
   
  # Shaded tiles for photoperiod
  geom_tile(data = pp_data, 
            mapping = aes(x = Time, fill = Photoperiod,y=0),
            linewidth = 0,
            alpha = 0.3,
            linetype = 0,
            height = Inf, # tiles will go all the way up and down
            show.legend = NA,
            inherit.aes = FALSE) + 
  scale_fill_manual(values = c("Dark" = "gray65",
                               "Light" = "white",
                               "Subjective Light" = "gray75"),guide = "none") + new_scale_fill() +
  stat_summary(data = ts,
               aes(x = Time, 
               y = .data[[var]],
               color = .data[[groupvar]],
               group = .data[[groupvar]]),
               fun = "mean", geom = "line", 
               linewidth = 1) + 
  stat_summary(data = ts,
               aes(x = Time, 
               y = .data[[var]],
               color = .data[[groupvar]],
               group = .data[[groupvar]],
               fill = .data[[groupvar]]),
               fun.data = mean_se, 
               geom = "ribbon", 
               alpha = 0.5, linetype = 0) + 
  scale_color_brewer(palette = plt) + 
  scale_fill_brewer(palette = plt) + 
  theme_classic() + 
  
  # Plot annotations and formatting
  labs(x = "Time (hours)", y = ylab) + 
  scale_x_continuous(expand = expansion(0, 0)) +   # no padding on the x-axis
  theme_classic() + 
  theme(text = element_text(size = 12))
}

tsploteach <- function(data,var,groupvar,facetvar,ylab) {
  
  ts <- data
  plot <- ggplot() +
    
    geom_tile(data = pp_data, 
              mapping = aes(x = Time, fill = Photoperiod,y=0),
              linewidth = 0,
              alpha = 0.3,
              linetype = 0,
              height = Inf, # tiles will go all the way up and down
              show.legend = NA,
              inherit.aes = FALSE) + 
    scale_fill_manual(values = c("Dark" = "gray65",
                               "Light" = "white",
                               "Subjective Light" = "gray75"),guide = "none") +
    
    #ggplot(ts, aes(x = Time, 
     #                      y = .data[[var]])) + 
    # Conditionally facet if facetvar is not NA
    {if(!is.na(facetvar) & facetvar %in% colnames(data))facet_grid(~ .data[[facetvar]])} +
    geom_line(data = ts, aes(x = Time,
                             y = .data[[var]],
                             color = Animal),
              alpha = 0.5,
              linewidth = 1) +
    theme_classic() + 
    
    # Plot annotations and formatting
    labs(x = "Time (hours)", y = ylab) + 
    scale_x_continuous(expand = expansion(0, 0)) +   # no padding on the x-axis
    theme_classic() + 
    theme(text = element_text(size = 12))
  return(plot)
}

# Create photoperiod df
pp_data <- df2plt %>%
    distinct(Time,Photoperiod,LightCycle) %>%
    mutate(Photoperiod = case_when(
      LightCycle == "LD" & Photoperiod == "Light" ~ "Light",
      LightCycle == "LD" & Photoperiod == "Dark" ~ "Dark",
      LightCycle == "DD" & Photoperiod == "Light" ~ "Subjective Light",
      LightCycle == "DD" & Photoperiod == "Dark" ~ "Dark"))
```

Generate plots

```{r}

# Get annotations from unitkeys
ylab <- filter(unitkeys,Renamed_Var == {{var}}) %>% 
    select(Title,Unit) %>% 
    summarize(ylab = paste(Title,Unit)) %>% 
    pull()
if (grepl("NA",ylab)) ylab <- title else ylab <- ylab
title <- filter(unitkeys,Renamed_Var == {{var}}) %>% 
    select(Title) %>%
    pull()

if (by_group == T) {
  p <- tsplot(df2plt,var,groupvar,facetvar,ylab)
  p
} else {
  p <- tsploteach(df2plt,var,groupvar,facetvar,ylab)
  p
}
```