The Most Long Gene

[efeaybuke]

Question

There are a lot of chromosomes and chromosomes are occurred negative and positive strands. These strands contain genes. So , how long are these genes? Which genes are longer than others? Please find gene sizes and show the longest 10 genes at the graphic for each strand.

Here is the result:

Here is the the human gene data set: download.file("https://s3-us-west-2.amazonaws.com/veri-analizi/hg19v2_clean.csv","hg19v2_clean.csv")
human_genes <- read_csv("hg19v2_clean.csv")

library(readr)
library(dplyr)
library(ggplot2)

download.file("https://s3-us-west-2.amazonaws.com/veri-analizi/hg19v2_clean.csv","hg19v2_clean.csv")
gene_data <- read_csv("hg19v2_clean.csv") 

long_gene <- gene_data %>% 
  mutate(size = end - start) %>% 
  arrange(desc(size))

negative_strand <- long_gene %>% 
  filter(strand=="-1") %>% 
  top_n(10)

positive_strand <- long_gene %>% 
  filter(strand=="1") %>% 
  top_n(10)

strands <- bind_rows(negative_strand, positive_strand)

strands %>% 
  mutate(gene_name = reorder(gene_name, size)) %>%
  ggplot(aes(x=gene_name, y=size, fill=strand)) +
  geom_col(show.legend = FALSE)+
  facet_wrap(~strand, scales = "free")+
  coord_flip()

Originality

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• [ ] Inspired
• [ ] Paraphrased or copied

Difficulty Level

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[alperyilmaz]

this can be done in single pipe actually. top_n or rank functions operate within groups defined by prior group_by function.

human_genes %>% 
  mutate(length=end-start) %>% 
  group_by(strand) %>% 
  top_n(10,length) %>% 
  ggplot(aes(x=reorder(gene_name, length), y=length, fill=as.factor(strand))) +
  geom_col(show.legend = FALSE) +
  facet_wrap(~strand , scales = "free")+
  coord_flip()