static_plate_reader_plotting_and_html.Rmd

---
author: "Prashant Kalvapalle"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: 
  html_document:
    theme: flatly
    toc: TRUE
    toc_float: TRUE
---

---
title: `r title_name`
---

```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(echo = F, message = F, warning = F, fig.width = 5, fig.height = 4)

```

## Plotting


### all fluorescence (normalized)

```{r allfluor}

plt_all_fluor <- ggplot(data = long_fluor.normalized_processed,
                  mapping = aes(y = Samples, x = value)) + 
  geom_jitter(width = 0, height = .3) + # plot individual replicates
  
  # plot mean as a vertical dash (for small point, use size = 0.5)
  geom_point(data = long_unique.normalized_processed,
             aes(x = mean), size = 5, shape = '|') + 
  # Indicate a light grey bar for the mean - to aid the eye
  geom_bar(data = long_unique.normalized_processed, 
           aes(x = mean, y = Samples), alpha = 0.3, fill = 'gray', stat = 'identity',position = 'dodge') +
  
  # facets
  facet_grid(~ Measurement, space = 'free', scale = 'free') +
    # geom_segment(aes(x = GFP_mean, xend = 0, yend = Samples), alpha = 0.1, colour = 'red') + 
  
  # Axis labels
  xlab('Value') + ylab('') + 
  
  # Plot title and subtitle
  ggtitle(str_c('Fluorescence measurement', if(MEFL_normalization) ' : in MEFL (uM)' else ' (a.u.)' ),
          subtitle = 'Plasmids')
  
plt_all_fluor_annotated <- 
  {plt_all_fluor + 
      geom_text(data = long_unique.normalized_processed,  
                mapping = aes(x = mean, label = mean %>% round, 
                              hjust = if_else(mean > max(mean)/2, 1.3, -0.3)))
  } %>% 
  print()

# showing GFP/OD and RFP/OD with equal width
plt_all_fluor_annotated +  facet_grid(~ Measurement, scale = 'free')

```


### Ordered: fluorescence and normalized

```{r rawgfp}

# Find all the fluoresce channels in the data (return as expression)
FPs <- colnames(processed.data) %>% str_subset('.FP$|OD$') %>% rlang::parse_exprs(.)


# Run the raw data plotter on each fluorescence : regular + interactive plot
map(FPs, plot_static_fluorescence)

```


``` {r child = if(run_dose_response_pipeline) 'dose_response_plots.Rmd'}
# child document format inspired from : https://bookdown.org/yihui/rmarkdown-cookbook/child-document.html
# `r if(run_dose_response_pipeline {"## Dose-response plots"})`
```


## Data tables

Baseline fluorescence that was subtracted before plotting 

``` {r datadisplay}
# kable(processed.data, caption = 'full data') # format with colours etc for good visualization

kable(empty_cells_baseline) # show baseline data

```

check for processed data as a csv file in the `/plate reader data/processed` folder