encode expression

setwd("/Users/ianglavin/Documents/bin501/week2")
myGex <- read.table("ENCFF166SFX.tsv", header = TRUE)

# this graph shows the distribution of gene lenghts across the ENCODE dataset
library(ggplot2)
ggplot(myGex, aes(x = length)) +
  geom_histogram(binwidth = 50, fill = "orange") +
  labs(title = "Distribution of Gene Lengths")

# The graph shows the distribution of gene lengths in the ENCODE brain tissue dataset, limited to genes shorter than 10,000 bases. Also shows that shorter genes are more common.
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

normalLength <- myGex |>
  filter(`length` < 10000)
ggplot(normalLength, aes(x = `length`)) +
  geom_histogram(binwidth = 1000, fill = "orange") +
  labs(title = "Modified Distribution of Gene Lengths")

# create a bar graph showing genes with high expression in the brain tissue sample.
hiEx <- myGex |>
  filter(FPKM > 5000)
ggplot(hiEx, aes(x = gene_id, y = FPKM, fill = FPKM)) +
  geom_col() +
  scale_fill_gradient(low = "orange", high = "red") +
  theme(axis.text.x = element_text(angle = 90, vjust = 1, hjust = 1)) +
  labs(title = "Highly Expressed Genes in Brain Tissue")

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