siRNA_metagene.Rmd

---
title: "metagene_siRNA"
author: "Chenxin Li"
date: "February 8, 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(stringr)
library(RColorBrewer)
library(svglite)
```

#load data
##upstream
```{r}
BS1_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/blender-sperm-1_S30_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE) 

BS2_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderSperm2_S8_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
     "\t", escape_double = FALSE, trim_ws = TRUE)

BS4a_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderSperm4a_S173_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS4b_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm4b_S176_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS6a_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm6a_S174_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS6b_up <-  read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm6b_S177_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BV1_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderVegetativeCell1_S4_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BV2_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderVegetativeCell2_S6_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B15_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-15_S26_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B20_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-20_S27_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B25_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-25_S28_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

ddm1_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ddm1ab.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

ddm1_con_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ddm1ab_control.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

drm2_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/drm2-T-DNA.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

drm2_con_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/drm2-T-DNA_control.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9a_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9a_S25_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9b_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9b_S26_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9c_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9c_S27_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E2_up <-  read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell2_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E3_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell3_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E4_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell4_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV1a_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ovary-no-egg-1a_S31_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV1b_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ovary-no-egg-1b_S32_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV2_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Ovarynoegg2_S5_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

P20_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Protoplast-20_S30_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

P25_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Protoplast-25_S31_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SD4_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/seedling4_S3_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SP5b_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/sperm-5b_S28_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SP5c_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/sperm-5c_S29_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

root_up <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/SRR5713891.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_upstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)
```
```{r}
B15_up <- B15_up %>% 
  mutate(sample_ID = "B15")

B20_up <- B20_up %>% 
  mutate(sample_ID = "B20")

B25_up <- B25_up %>% 
  mutate(sample_ID = "B25")

BS1_up <- BS1_up %>% 
  mutate(sample_ID = "BS1")

BS2_up <- BS2_up %>% 
  mutate(sample_ID = "BS2")

BS4a_up <- BS4a_up %>% 
  mutate(sample_ID = "BS4a")

BS4b_up <- BS4b_up %>% 
  mutate(sample_ID = "BS4b")

BS6a_up <- BS6a_up %>% 
  mutate(sample_ID = "BS6a")

BS6b_up <- BS6b_up %>% 
  mutate(sample_ID = "BS6b")

BV1_up <- BV1_up %>% 
  mutate(sample_ID = "BV1")

BV2_up <- BV2_up %>% 
  mutate(sample_ID = "BV2")

ddm1_up <- ddm1_up %>% 
  mutate(sample_ID = "ddm1")

ddm1_con_up <- ddm1_con_up %>% 
  mutate(sample_ID = "ddm1_con")

drm2_up <- drm2_up %>% 
  mutate(sample_ID = "drm2")

drm2_con_up <- drm2_con_up %>% 
  mutate(sample_ID = "drm2_con")

E2_up <- E2_up %>% 
  mutate(sample_ID = "E2")

E3_up <- E3_up %>% 
  mutate(sample_ID = "E3")

E4_up <- E4_up %>% 
  mutate(sample_ID = "E4")

E9a_up <- E9a_up %>% 
  mutate(sample_ID = "E9a")

E9b_up <- E9b_up %>% 
  mutate(sample_ID = "E9b")

E9c_up <- E9c_up %>% 
  mutate(sample_ID = "E9c")

OV1a_up <- OV1a_up %>% 
  mutate(sample_ID = "OV1b")

OV1b_up <- OV1b_up %>% 
  mutate(sample_ID = "OV1b")

OV2_up <- OV2_up %>% 
  mutate(sample_ID = "OV2")

P20_up <- P20_up %>% 
  mutate(sample_ID = "P20")

P25_up <- P25_up %>% 
  mutate(sample_ID = "P25")

root_up <- root_up %>% 
  mutate(sample_ID = "root")

SD4_up <- SD4_up %>% 
  mutate(sample_ID = "SD4")

SP5b_up <- SP5b_up %>% 
  mutate(sample_ID = "SP5b")

SP5c_up <- SP5c_up %>% 
  mutate(sample_ID = "SP5c")

upstream <- rbind(B15_up, B20_up, B25_up, BS1_up, BS2_up, BS4a_up, BS4b_up,
                  BS6a_up, BS6b_up, BV1_up, BV2_up, ddm1_up, ddm1_con_up, drm2_up, drm2_con_up,
                  E2_up, E3_up, E4_up, E9a_up, E9b_up, E9c_up, OV1a_up, OV1b_up, OV2_up,
                  P20_up, P25_up, root_up, SP5b_up, SP5c_up) %>% 
  mutate(location = "5' end")
```

##downstream
```{r}

BS1_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/blender-sperm-1_S30_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE) 

BS2_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderSperm2_S8_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
     "\t", escape_double = FALSE, trim_ws = TRUE)

BS4a_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderSperm4a_S173_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS4b_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm4b_S176_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS6a_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm6a_S174_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BS6b_down <-  read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Blendersperm6b_S177_L007_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BV1_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderVegetativeCell1_S4_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

BV2_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/BlenderVegetativeCell2_S6_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B15_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-15_S26_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B20_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-20_S27_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

B25_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Bulk-25_S28_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

ddm1_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ddm1ab.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

ddm1_con_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ddm1ab_control.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

drm2_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/drm2-T-DNA.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

drm2_con_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/drm2-T-DNA_control.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9a_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9a_S25_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9b_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9b_S26_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E9c_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/egg-9c_S27_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E2_down <-  read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell2_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E3_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell3_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

E4_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/eggcell4_combined.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV1a_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ovary-no-egg-1a_S31_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV1b_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/ovary-no-egg-1b_S32_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

OV2_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Ovarynoegg2_S5_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

P20_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Protoplast-20_S30_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

P25_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/Protoplast-25_S31_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SD4_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/seedling4_S3_L004_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SP5b_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/sperm-5b_S28_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

SP5c_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/sperm-5c_S29_L002_R1_001.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)

root_down <- read_delim("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/metagene_siRNA_coverage/metagene_siRNA_coverage_Feb7/metagene/SRR5713891.fastq.gz.trimmed.fastq.gz_MSU7_filtered_genes.gff_q20_downstream.txt", 
    "\t", escape_double = FALSE, trim_ws = TRUE)
```
```{r}
B15_down <- B15_down %>% 
  mutate(sample_ID = "B15")

B20_down <- B20_down %>% 
  mutate(sample_ID = "B20")

B25_down <- B25_down %>% 
  mutate(sample_ID = "B25")

BS1_down <- BS1_down %>% 
  mutate(sample_ID = "BS1")

BS2_down <- BS2_down %>% 
  mutate(sample_ID = "BS2")

BS4a_down <- BS4a_down %>% 
  mutate(sample_ID = "BS4a")

BS4b_down <- BS4b_down %>% 
  mutate(sample_ID = "BS4b")

BS6a_down <- BS6a_down %>% 
  mutate(sample_ID = "BS6a")

BS6b_down <- BS6b_down %>% 
  mutate(sample_ID = "BS6b")

BV1_down <- BV1_down %>% 
  mutate(sample_ID = "BV1")

BV2_down <- BV2_down %>% 
  mutate(sample_ID = "BV2")

ddm1_down <- ddm1_down %>% 
  mutate(sample_ID = "ddm1")

ddm1_con_down <- ddm1_con_down %>% 
  mutate(sample_ID = "ddm1_con")

drm2_down <- drm2_down %>% 
  mutate(sample_ID = "drm2")

drm2_con_down <- drm2_con_down %>% 
  mutate(sample_ID = "drm2_con")

E2_down <- E2_down %>% 
  mutate(sample_ID = "E2")

E3_down <- E3_down %>% 
  mutate(sample_ID = "E3")

E4_down <- E4_down %>% 
  mutate(sample_ID = "E4")

E9a_down <- E9a_down %>% 
  mutate(sample_ID = "E9a")

E9b_down <- E9b_down %>% 
  mutate(sample_ID = "E9b")

E9c_down <- E9c_down %>% 
  mutate(sample_ID = "E9c")

OV1a_down <- OV1a_down %>% 
  mutate(sample_ID = "OV1b")

OV1b_down <- OV1b_down %>% 
  mutate(sample_ID = "OV1b")

OV2_down <- OV2_down %>% 
  mutate(sample_ID = "OV2")

P20_down <- P20_down %>% 
  mutate(sample_ID = "P20")

P25_down <- P25_down %>% 
  mutate(sample_ID = "P25")

root_down <- root_down %>% 
  mutate(sample_ID = "root")

SD4_down <- SD4_down %>% 
  mutate(sample_ID = "SD4")

SP5b_down <- SP5b_down %>% 
  mutate(sample_ID = "SP5b")

SP5c_down <- SP5c_down %>% 
  mutate(sample_ID = "SP5c")

downstream <- rbind(B15_down, B20_down, B25_down, BS1_down, BS2_down, BS4a_down, BS4b_down,
                  BS6a_down, BS6b_down, BV1_down, BV2_down, ddm1_down, ddm1_con_down, drm2_down, drm2_con_down,
                  E2_down, E3_down, E4_down, E9a_down, E9b_down, E9c_down, OV1a_down, OV1b_down, OV2_down,
                  P20_down, P25_down, root_down, SP5b_down, SP5c_down) %>% 
  mutate(location = "3' end")

```
##sample des, library size
```{r}
sample_des <- read_excel("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/sample_des.xlsx") 

siRNA_comp <- read_excel("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/TE/siRNA_comp.xlsx")

total_siRNA_length <- read_excel("C:/Users/cxli9/Desktop/Li/PBI/PBI299 (Sundar Lab)/smRNA project/CLVS08/TE/total_siRNA_length.xlsx") 
```
```{r}
sample_des_size <- siRNA_comp %>% 
  select(-library) %>% 
  inner_join(sample_des, by = "sample_ID") %>% 
  select(-X2, -X3, -X4, -X5, -X6) %>% 
  inner_join(total_siRNA_length, by = "sample_ID")

sample_des_size
```

#normalize
```{r}
meta <- rbind(upstream, downstream) %>% 
  mutate(location = factor(location, levels = c("5' end", "3' end"))) %>% 
  inner_join(sample_des_size, by = "sample_ID") %>% 
  mutate(pro_24 = `total overlap`/ `24nt`) %>% 
  mutate(pro_sm = `total overlap`/ lib.size) %>% 
  mutate(pro_si = `total overlap`/ total.siRNA)

meta
```


#plot
```{r}
pal <- c("tomato1", "darkgreen", "orangered3", "orange", "grey40", "seagreen", "turquoise4", "violetred2")
pal3 <- pal3 <- c("tomato1", "seagreen", "dodgerblue2")
```

```{r}
#norm by 24nt 

meta %>% 
  filter(genotype == "WT") %>% 
  ggplot(aes(x = `bin start`, y = pro_24)) +
  facet_grid(.~location, scales = "free_x")+
  stat_summary(geom = "line", fun.y = mean, aes(group = sample_type, color = sample_type), size = 1, alpha = 0.8) +
  #stat_summary(geom = "linerange",  fun.data = "mean_cl_boot", aes(color = sample_type)) +
  scale_x_continuous(breaks = c(-3000,-1500, 0, 1500, 2900), labels = c("-3KB", "", "*", "", "polyA+3KB"))+
  scale_color_manual(values = pal) +
  labs(color = NULL,
       x = "relative location", 
       y = "normalized coverage") + 
  theme_minimal()+
  theme(text = element_text(size = 14, face="bold")) +
  theme(axis.text.x=element_text(colour="black")) +
  theme(axis.text.y=element_text(colour="black"))

ggsave(filename = "24_meta_WT.png")
  
```
```{r}
meta %>% 
  filter(genotype == "WT") %>% 
  filter(sample_type == "egg"|
           sample_type == "sperm"|
           sample_type == "seedling shoot") %>% 
  ggplot(aes(x = `bin start`, y = pro_si * 1000)) +
  facet_grid(.~location, scales = "free_x")+
  stat_summary(geom = "line", fun.y = mean, aes(group = sample_type, color = sample_type), size = 1.25, alpha = 0.8) +
  #stat_summary(geom = "linerange",  fun.data = "mean_cl_boot", aes(color = sample_type)) +
  scale_x_continuous(breaks = c(-3000,-2000,-1000, 0, 1000, 2000, 2900),
                     labels = NULL)+
  scale_color_manual(values = pal3) +
  labs(color = NULL,
       x = NULL, 
       y = "normalized coverage") + 
  theme_minimal()+
  theme(legend.position = c(0.8, 0.8)) +
  theme(text = element_text(size = 18, face="bold")) +
  theme(axis.text.x=element_text(colour="black")) +
  theme(axis.text.y=element_text(colour="black"))

ggsave(filename = "24_meta_gamate.svg", height = 4, width = 5)
```

```{r}
meta_m <- meta %>% 
  filter(sample_type == "leaf") %>% 
  mutate(rows = case_when(
    str_detect(sample_ID, "ddm") ~ "ddm1ab leaf",
    str_detect(sample_ID, "drm") ~ "drm2 leaf"
  )) 
```

```{r}
meta_m %>% 
  filter(sample_type == "leaf") %>% 
  ggplot(aes(x = `bin start`, y = pro_si * 1000)) +
  facet_grid(rows ~ location, scales = "free_x")+
  geom_line(aes(color = genotype), size = 1, alpha = 0.7) +
  # stat_summary(data = meta %>% 
  #                filter(sample_type == "egg cell" |
  #                         sample_type == "sperm cell"), 
  #   geom = "line", fun.y = mean, aes(group = sample_type, color = sample_type), size = 1, alpha = 0.8) +
  scale_x_continuous(breaks = c(-3000,-2000,-1000, 0, 1000, 2000, 2900),
                     labels = NULL)+
  scale_color_manual(values = c("red", "blue", "grey40")) +
  labs(color = NULL,
       x = NULL, 
       y = "normalized coverage") + 
  theme_minimal()+
  theme(legend.position = c(0.85, 0.4), strip.text.y = element_blank())+
  theme(text = element_text(size = 18, face="bold")) +
  theme(axis.text.x=element_text(colour="black")) +
  theme(axis.text.y=element_text(colour="black")) 

ggsave(filename = "ddm1 and drm2 24_meta_WT.svg", height = 4, width = 5)
```



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