README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  fig.height=8,
  fig.width=8 ,
  message = FALSE
)
```

```{r , message=FALSE, echo=FALSE}
library(magrittr)
```
# corplot 
<!-- badges: start -->

```{r , echo=FALSE , results='asis' , message=FALSE}
cat(
badger::badge_devel("cparsania/corplot" , color = "blue"),
badger::badge_lifecycle()
  
)

```
<!-- badges: end -->

## Motivation

 Genomics data often stored in a matrix like format, where each row is a feature (gene, transcript, protein etc.) and columns are  variables (e.g. signal intensity of experiments such as RNA-seq, ChIP-seq, Pol-II ChIP-seq etc.). Variables are often grouped by replicates, time-points or specific experimental conditions such as wild type, deletion, control, treatment etc. In such a multidimensional data, plotting a x-y scatter plot between different groups require lots of data wrangling before it goes for final ggplot. 
 
 `corplot` has functions to generate heatbox and pairwise scatter plots directly from feature matrix given in a tbl format. Let's have a look into required input data and resultant plots out of `corpot`. 

## Install

```{r , eval=FALSE}
if(require("devtools")){
        devtools::install_github("cparsania/corplot")
} else{
        install.packages("devtools")
        devtools::install_github("cparsania/corplot")
}

```

## Correlation heatbox 

## All samples vs all samples

```{r, fig.width=6,fig.height=4}

expr_mat_file <- system.file("extdata" ,"example_data_expr_mat_01.txt" , package = "corplot")
expr_mat <- readr::read_delim(expr_mat_file , delim = "\t") 

expr_mat

## calculate  pairwise correlation 
cor_tbl <- corplot::get_pairwise_cor_tbl(expr_mat , var = "gene_name" , method = "pearson") 

cor_tbl

cp <- corplot::get_corr_heat_box(cor_tbl,var1 = var1, var2 = var2 ,value = corr) 
cp + viridis::scale_fill_viridis() + ggplot2::theme(axis.text.x = ggplot2::element_text(angle=90))

```

## Group by replicates

All samples vs all samples correlation heatbox has redundant samples on each axis. This makes plot less readable. Alternate way to overcome this is to plot samples of replicate 1 vs samples of replicate 2.    

```{r, fig.width=5, fig.height=3}
cor_tbl2 <- cor_tbl %>% dplyr::filter(grepl("Rep.A", var1) ) %>%  dplyr::filter(grepl("Rep.B", var2) )

cor_tbl2

corplot::get_corr_heat_box(cor_tbl2,var1 = var1, var2 = var2, value = corr) + 
  viridis::scale_fill_viridis() 

```

## Scatter plot 

## Group by replicates : All combinations 

``` {r}
groups_file <- expr_mat_file <- system.file("extdata" ,"example_data_01_sample_groups.txt" , package = "corplot")
groups <- readr::read_delim(file = groups_file,delim = "\t") 

groups 

csp <- corplot::get_pair_wise_scatter(dat_tbl = expr_mat, group_tbl = groups,var_plot = condition, var_plot_group = repl,dat_id = gene_name)

csp
```

### Display corr value

```{r}

cor_tbl2 <- cor_tbl %>% dplyr::rename(`Rep.A`=var1, `Rep.B` = var2) %>% 
  dplyr::filter(grepl("Rep.A" ,`Rep.A`)) %>%
  dplyr::filter(grepl("Rep.B" ,`Rep.B`)) %>% 
  TidyWrappers::tbl_replace_string("_.*" , "")

cor_tbl2

csp + ggplot2::geom_text(data = cor_tbl2,  x = 4, y = 18, ggplot2::aes(label = paste("r","=",corr , sep = "")) , 
                         fontface="italic" , col = "red",size = 5)


```

## Group by replicates : Only replicate pairs  
```{r}
csp2 <- corplot::get_pair_wise_scatter(dat_tbl = expr_mat, group_tbl = groups,var_plot = condition, var_plot_group = repl,dat_id = gene_name,view_matrix = FALSE)

csp2
```

### Display corr value

``` {r, fig.width = 5, fig.height = 5}
cor_tbl3 <- cor_tbl2 %>% dplyr::filter(`Rep.A` == `Rep.B`) 
csp3 <- corplot::get_pair_wise_scatter(dat_tbl = expr_mat, group_tbl = groups,var_plot = condition, var_plot_group = repl,dat_id = gene_name,view_matrix = FALSE)

csp2 + ggplot2::geom_text(data = cor_tbl3,  x = 3, y = 18, ggplot2::aes(label = paste("r","=",corr , sep = "")) , 
                         fontface="italic" , col = "red")

```