Week8: Loops

R-intermediate
Author

Tien-Cheng

Welcome to the eighth course! You will learn more about for-loop and data visualization:

Learning goals
  1. requirements of merging dataframes
  2. save or show the result of for loop
  3. ggplot()
Discussion
  1. What is the component for-loop? How to check if it works for each element?
  2. what are long and wide? when to use what?

1 Student’s data

practice with files from data/student.

1.1 How to save the column names of all files in a directory to a list using for loop?

For loop concept 

path <- "./data/student/"
filenames <- list.files(path,pattern=".xlsx")
#create empty list
df <- vector(mode="list",length=length(filenames))

for(i in 1:length(filenames)){
  fullpath <- paste0(path,filenames[i])
  df[[i]] <- xlsx::read.xlsx(fullpath,
                             sheetIndex = 1) %>% 
    names()
}

df

1.2 How to name list elements based on student’s name ?

$clement
[1] "Var"          "Plot_Id"      "Spikes"       "flower"       "kernal.full" 
[6] "Kernal.half"  "kernal.small"

$hanwenhsu
[1] "var"          "plot_id"      "spike"        "flower"       "kernel.full" 
[6] "kernel.half"  "kernel.small"

$shawon
[1] "var"         "plot.id"     "spike"       "flower"      "kernel.full"
[6] "kernel.half" "NA."        
student_name <-   purrr::map_chr(filenames,  ~{
  .x %>% strsplit("_") %>% unlist() %>% 
    .[4] %>% sub(".xlsx","",.)
}) 
names(df) <-student_name
df

1.3 How to combine all the dataframe by row?

If you know the column names are different, can you still combine them?

df<- map_dfr(list.files("./data/student"),~{
  
  file<- xlsx::read.xlsx(paste0("./data/student/",.x),sheetIndex = 1)
})
df %>% 
  glimpse()
Rows: 0
Columns: 0

Here are possible steps:

  • observe the patterns of column names, how to unify the column names?
  • replace “kernal” with “kernel”
  • replace “spikes” with “spike”
  • replace “plot.id” with “plot_id”
  • how to add the student’s name as a column? where should you put it in the for-loop body?
  • how to fill the missing cultivar and plot_id?
  • remove “na.” column check your loop-body with the first element in your range.
Rows: 57
Columns: 8
$ var          <chr> "Capone", "Capone", "Capone", "Capone", "Capone", "Capone…
$ plot_id      <dbl> 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 159, 15…
$ spike        <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17…
$ flower       <dbl> 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, …
$ kernel.full  <dbl> 0, 2, 2, 2, 3, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 1, …
$ kernel.half  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ kernel.small <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ student      <chr> "clement", "clement", "clement", "clement", "clement", "c…
library(magrittr)
df<- map_dfr(list.files("./data/student"),~{
  
  student_name <-  .x %>% strsplit("_") %>% unlist() %>% 
    .[4] %>% sub(".xlsx","",.)
  
  file<- xlsx::read.xlsx(paste0("./data/student/",.x),sheetIndex = 1) %>%  
    `colnames<-`(stringr::str_to_lower(names(.)))%>% 
    `colnames<-`(gsub("kernal","kernel",names(.))) %>% 
    `colnames<-`(gsub("spikes","spike",names(.)))%>%
    `colnames<-`(gsub("plot.id","plot_id",names(.))) %>% 
    mutate(student=student_name)
}) 
df %<>% mutate(var="Capone",plot_id=159) %>% 
  .[!grepl("na.",names(.))]
df %>% glimpse()

This answer is written in map_() series, could you rewrite in for loop?

1.4 How to visualize the result?

Practice to make a draft, what will be the x and y, what will be the color?

Is there difference between geom_line() and geom_path()?

Line Plot 1

Line Plot 2
# line plot 1
df %>% 
  group_by(student,spike) %>% 
  ggplot(aes(flower,spike,color=student))+
  geom_line(alpha=.5)+
  theme(legend.position = "bottom")
# line plot 2
df %>% 
  group_by(student,spike) %>% 
  ggplot(aes(flower,spike,color=student))+
  geom_point()+
  geom_path(alpha=.5)+
  theme(legend.position = "bottom")

2 recommendation

Advanced R: control flow