06_BasicNotebook.Rmd

---
output: html_document
---


```{r Setup, setup, include=FALSE}
knitr::opts_chunk$set(message = FALSE, echo = FALSE, warning = FALSE)
```

```{r, message = FALSE}
library(data.table)
library(tidyverse)
library(kableExtra)
library(reactable)
library(htmltools)
library(ggpubr)
```

```{r}
table <- fread("data_input/test01_input.csv")
file_id <- "test"
```


# Report for experiment `r file_id` {.tabset .tabset-fade .tabset-pills}


## Boxplot 

```{r}
#calculating yield in 3 different ways:
table <- table[,yield01:=elute.vol*Q.conc][]
table$yield02 <- table$elute.vol*table$Q.conc
table <- table %>% mutate(yield03 = elute.vol*Q.conc)
```

```{r}
ggplot(table, aes(x=reformatter, y=Q.conc, color=plate)) +
  geom_boxplot(outlier.colour = 'grey', outlier.alpha = 0.5)
```

## Slopes

```{r}
#alternative way of calculating max per plate and slope using tidyverse:
table <- table %>%
  group_by(`96w.pos`) %>%
  mutate(plate.max = max(Q.conc)) 

table <- table %>%
  mutate(new.plate.slope = case_when(
    Q.conc==plate.max ~ plate,
    TRUE ~ "eppen_221123"
  ))
```

```{r}
#a better way avoiding hardcoded names
widetable <- table %>% 
  select(plate, `96w.pos`, Q.conc)  %>% 
  spread(plate, Q.conc)

widetable$plate.slope <- colnames(widetable)[apply(widetable,1,which.max)]

table <- left_join(table, widetable)
```

```{r}
plot <- ggplot(table, aes(x=plate, y=Q.conc)) +
  geom_point(aes(fill=plate)) + 
  geom_line(aes(group=`96w.pos`, color=plate.slope)) +
  labs(x='Reformatted by whom', y='Extraction concentration (ng/uL)')
```

#### Summary Table

```{r}
summary_table <- widetable %>%
  group_by(plate.slope) %>%
  summarise(samples = n())

summary_table_formatted <- ggtexttable(summary_table, rows = NULL, theme = ttheme("blank"))
```

```{r, fig.height=6, fig.width=9}
ggarrange(plot, summary_table_formatted, ncol=2, widths=c(3,1))
```

## Table 

```{r, fig.width=9}
htmltools::browsable(
  tagList(
    tags$button(
      tagList(fontawesome::fa("download"), "Download as CSV"),
      onclick = "Reactable.downloadDataCSV('table-download', 'table.csv')"
    ),
    table %>%
      reactable(filterable = TRUE,
                pagination = FALSE,
                searchable = TRUE,
                elementId = "table-download")
  )
)
```

# 
::: {#box style="color: white; background-color:red; font-size: 20px; text-align:center; font-weight: bold;"}
To run as an automatic report use the script [run_Notebook.R](run_Notebook.R)
:::