rice_1st_nucleotide_preferences.Rmd

---
title: "First_nucleotide_preferences"
author: "Chenxin Li"
date: "January 14, 2019"
output:
  html_notebook:
    number_sections: yes
    toc: yes
    toc_float: yes
  html_document:
    toc: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(ggplot2)
library(emmeans)
library(tidyr)
library(dplyr)
library(readr)
library(readxl)
library(vegan)
library(edgeR)
library(RColorBrewer)
library(svglite)
```
#1st nucleotide preferences by length
```{r}
first_n <- read_excel("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/first_nucleotide_pre/rice_siRNA_1st_nt_by_length.xlsx")
first_n
```
```{r}
first_n_l <- first_n %>% 
  gather("nucleotide", "proportion", 3:6) %>% 
  mutate(nt = as.factor(length)) %>% 
  mutate(nucleotide = factor(nucleotide, levels = c("A", "C", "G", "U")))

first_n_l %>% 
  group_by(sample_type, length) %>% 
  arrange(desc(nucleotide))

#first_n_l[order(first_n_l$nucleotide, decreasing = T), ]
```
```{r}
first_n_l  %>% 
  ggplot(aes(x = sample_type, y = proportion)) +
  facet_grid(. ~ nt, scales = "free") +
  geom_bar(stat = "identity", aes(fill = nucleotide), position = position_stack(reverse = T)) +
  labs(x = NULL,
       fill = NULL) +
  scale_fill_brewer(palette = "Set2") +
  scale_x_discrete(label = c("egg", "ovary", "pollen VC", "sd shoot", "sperm")) +
  theme_minimal()+
  theme(text = element_text(size = 14, face="bold")) +
  theme(axis.text.x = element_text(colour="black", angle = 45, hjust = 1)) +
  theme(axis.text.y = element_text(colour="black"))

ggsave(filename = "first_nucleotide.png")
```
```{r} 
#egg sperm seedling only
first_n_l  %>%
  filter(sample_type == "egg" |
           sample_type == "seedling" |
           sample_type == "sperm") %>%
  ggplot(aes(x = sample_type, y = proportion)) +
  facet_grid(. ~ nt, scales = "free") +
  geom_bar(stat = "identity", aes(fill = nucleotide), position = position_stack(reverse = T)) +
  labs(x = NULL,
       fill = NULL, 
       y = NULL) +
  scale_fill_brewer(palette = "Set2") +
  theme_minimal()+
  theme(legend.position = "bottom") +
  theme(text = element_text(size = 18, face="bold")) +
  theme(axis.text.x = element_text(colour="black", angle = 45, hjust = 1)) +
  theme(axis.text.y = element_text(colour="black"))

ggsave(filename = "first_nucleotide_ECSDSP.svg", width = 3.5, height = 4.3)
```
#by tissue specificity
```{r}
first_by_bin <- read_excel("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/first_nucleotide_pre/rice_siRNA_1st_nt_by_bin_type.xlsx")
```
```{r}
first_by_bin
```
```{r}
first_by_bin_l <- first_by_bin %>% 
  gather("nucleotide", "proportion", 4:7) %>% 
  mutate(nt = as.factor(length)) %>% 
  mutate(nucleotide = factor(nucleotide, levels = c("A", "C", "G", "U"))) %>% 
  group_by(sample_type, length) %>% 
  arrange(desc(nucleotide))
```
```{r}
first_by_bin_l %>%
  mutate(loci = case_when(
    str_detect(bin, "egg") ~ "egg-\nspecific\nloci",
    str_detect(bin, "seedling") ~ "seedling\nshoot-\nspecific\nloci",
    str_detect(bin, "sperm") ~ "sperm-\nspecific\nloci",
    str_detect(bin, "intersect") ~ "intersect."
    )) %>% 
  mutate(loci_f = factor(loci, levels = c(
    "egg-\nspecific\nloci", 
    "seedling\nshoot-\nspecific\nloci",
    "sperm-\nspecific\nloci",
    "intersect."
  ))) %>%
  filter(loci_f != "intersect.") %>% 
  ggplot(aes(x = sample_type, y = proportion)) +
  #facet_grid(. ~ loci_f, scales = "free", space = "free") +
  geom_bar(stat = "identity", aes(fill = nucleotide), position = position_stack(reverse = T)) +
  labs(x = NULL,
       fill = NULL) +
  scale_fill_brewer(palette = "Set2") +
  scale_x_discrete(labels = c("egg", "seedling", "sperm")) +
  theme_minimal()+
  theme(text = element_text(size = 18, face="bold")) +
  theme(axis.text.x = element_text(colour="black", angle = 45, hjust = 1)) +
  theme(axis.text.y = element_text(colour="black"))

ggsave(filename = "first_nucleotide_by_specificity.svg", width = 3, height = 5)
```


Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.