---
title: "Patrycja_data_wrangling"
author: "Semra Smajic"
date: "11/4/2021"
output: html_document
---
## Load the packages
```{r}
library(plyr)
#library(readr)
library(tidyverse)
#library(stringr)
library(dplyr)
#library(ggplot2)
#library(ggpubr)
#library(Hmisc)
#library(reshape2)
```

## Load the data file. Please make sure of the correct separator in your file (sep = ",")
```{r}
dataset <- read.csv("U:/Projects/3. Comparison of astrocytic protocols/10. Data included in the paper/Fig. 2/raw data/Palm_GFAPperNucdata_version2_mod.csv", header = TRUE, sep = ",");

```


## Basic operations on columns - data calculation
# This is creating a new column (MyNewResult) with new data that you will calculate
```{r}
dataset$MyNewResult <- dataset$AreaNuclei/dataset$SkelArea;

write.csv(dataset, "C:/Users/semra.smajic/Desktop/MySavedDataset.csv")  # Always rename your .csv file

```


## Data grouping and analysis
# https://bookdown.org/manishpatwal/bookdown-demo/basic-operations-in-r.html
# var - variance
# sd- standard deviation
# mean - mean
# sum - summary
```{r}
analyzed_dataset <- dataset %>% 
  #group_by(Well, Field) %>%    # two levels of grouping
  group_by(CellLine, Replicate) %>%        # one level of grouping
  summarise(GFAPClass_mean = (mean(GFAPClass))
            )
write.csv(analyzed_dataset, "U:/Projects/3. Comparison of astrocytic protocols/10. Data included in the paper/Fig. 2/analyzed data/SummaryNuc_version2_mod_Palm.csv")    # Always rename your .csv file

```