151007_Transcript_length_histogram.Rmd

---
title: "Transcript Length Histogram"
author: "Garrett Graham"
date: "10/7/2015"
output: html_document
---

```{r global-options, include=FALSE}
knitr::opts_chunk$set(fig.width=7, fig.height=3, fig.path="./Transcript_length_histogram_figures/",
                      echo=FALSE, warning=FALSE, message=FALSE, dev="cairo_ps", dpi=300)
```

```{r libraries, echo=FALSE, include=FALSE}
require(GenomicRanges)
require(GenomicFeatures)
require(Gviz)
require(org.Hs.eg.db)
require(wesanderson)
require(ggplot2)
```

```{r load-dat, echo=FALSE, include=FALSE}
load("./transcript_sequences.RData")
df<-data.frame(Length = c(width(hq_seq), width(hg19_seq)), Source = c(rep("PacBio", length(hq_seq)), rep("RefSeq", length(hg19_seq))))
```

```{r ggplot}
a<-ggplot(df, aes(x = Length, y = ..density.., fill = Source, col = Source))
a<-a+geom_histogram(, binwidth=100, position="identity", alpha = 0.2)
a<-a+geom_freqpoly(binwidth=200, alpha = 1)
a<-a+xlim(c(200, 12000))
a<-a+ylab("Density")
a<-a+scale_color_manual(values = wes_palette("Zissou")[c(2, 4)])
a<-a+scale_fill_manual(values = wes_palette("Zissou")[c(2, 4)])
a<-a+theme_bw()
plot(a)
```