loops_conditions.qmd

---
bibliography: references.bib
number-sections: true
suppress-bibliography: false
---

# Loops and Conditions in R

```{r}
#| results: "asis"
#| echo: false
source("_common.R")
```

## Introduction

Importing data is often the first step in a data analysis project. Quality and integrity of imported data is key for the subsequent analysis - *Quality In Quality Out*. A good overview of data import in R helps to ensure integrity, completeness and efficient import of data .

## Libraries

```{r}
#| label: load-lib
#| echo: true
#| message: false
library(here)
library(tidyverse)
library(readxl)
```

## For loops

```{r}
#| label: for_loops
#| echo: true
#| message: false

for (i in c(1,2,3,4,5)) {
  print(paste0("here number ", i, "-)"))
  print(glue("here number {i}")) 
}

```

## Import multiple sheets from an EXCEL file

First let's test importing one sheet. We need the name of the file and sheet
```{r}
#| label: read-xlsx
#| echo: false
#| message: true
mysheet1 <- readxl::read_excel(path = here("data/Test.xlsx"), sheet = "Sheet1") 

```

Now we get a list of sheets in an Excel file

```{r}
#| label: read-xlsx
#| echo: false
#| message: true

my_sheets <- readxl::excel_sheets(here("data/Test.xlsx"))
my_sheets
```


Now we import all of the sheets using a for loop

```{r}
#| label: loop-through-sheets
#| echo: false
#| message: true

for (sheet_name in my_sheets) {
  mysheet <- readxl::read_excel(path = here("data/Test.xlsx"), sheet = sheet_name) 
  print(mysheet)
}

```
However, while each sheet is imported and was printed out, the tables  have not been joined yet. 

```{r}
#| label: loop-through-sheets
#| echo: false
#| message: true

for (sheet_name in my_sheets) {
  
  mysheet <- readxl::read_excel(path = here("data/Test.xlsx"), sheet = sheet_name) 
  print(mysheet)
  
}

```

```{r}
#| label: loop-through-sheets
#| echo: false
#| message: true


# in the first loop data will be stacked to an empty dataframe. So we need to define it first
final_table <- tibble()

for (sheet_name in my_sheets) {
  
  mytable <- readxl::read_excel(path = here("data/Test.xlsx"), sheet = sheet_name) 
  # Add sheet name as column
  mytable <- mytable |> mutate(sheet = sheet_name, .before = ID)
  
  # Stack the table to the current stacked 
  final_table <- bind_rows(final_table, mysheet)
  
}
```


```{r}
# define function

get_my_table <- function(filename, sheetname) {
    mysheet <- readxl::read_excel(filename, sheet = sheetname) 
    mysheet <- mysheet |> mutate(sheet = sheet_name, .before = ID)
    # return result by calling it
    mysheet
}


my_sheets <- readxl::excel_sheets(here("data/Test.xlsx"))

for (sheet_name in my_sheets) {
  
  mysheet <- get_my_table(filename = here("data/Test.xlsx") ,sheetname = sheet_name)
  
  final_table <- bind_rows(final_table, mysheet)
  
}
```


```{r}
library(purrr)

myfunction <- function(x){print(x^2)}

a <- purrr::walk(.x =  c(1,2,3,4,5), .f = ~ myfunction(.x))


my_sheets <- readxl::excel_sheets(here("data/Test.xlsx"))

# Define function
get_my_table <- function(filename, sheetname) {
    mysheet <- readxl::read_excel(filename, sheet = sheetname) 
    mysheet <- mysheet |> mutate(sheet = sheet_name, .before = ID)
    # return result by calling it
    mysheet
}

#walk along the list of sheets, import them and bind them automatically

purrr::map_df(.x = my_sheets ,.f = ~get_my_table(here("data/test.xlsx"),sheetname = .x))
```


```{r}


sometext = "RQC"


if (str_detect(sometext, "TQC")) {
  print("Yes TQC")
} else if (str_detect(sometext, "BQC")) {
  print("yes BQC")
} else {
  print("nothing")
}

#...mutate( conc = if_else(tissue = "cells", conc *1000, conc)
        

ifelse("cells" == NA, 1,2)


qctype <- "PQC"

conc <- case_when(
  qctype == "TQC" ~ 0,
  qctype == "BQC" ~ 10,
  qctype == "RQC" ~ 100,
  qctype == "SPL" ~ 1000,
  TRUE ~ 1111
)


```