Last updated: 2022-11-01
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Knit directory:
locust-phase-transition-RNAseq/
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This document was written in R Markdown, and translated into html
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library("knitr")
library("rmdformats")
library("tidyverse")
library("DT") # for making interactive search table
library("plotly") # for interactive plots
library("ggthemes") # for theme_calc
library("reshape2")
## Global options
options(max.print="10000")
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE,
cache = FALSE,
comment = FALSE,
prompt = FALSE,
tidy = TRUE
)
opts_knit$set(width=75)STAR mapping to own
species# Load our SRA metadata table
metaseq <- read_table("data/metadata/RNAseq_modified_METADATA2022.txt", col_names = TRUE,
guess_max = 5000)
## Create an interactive search table
metaseq %>%
datatable(extensions = "Buttons", options = list(dom = "Blfrtip", buttons = c("copy",
"csv", "excel"), lengthMenu = list(c(10, 20, 50, 100, 200, -1), c(10, 20,
50, 100, 200, "All"))))mycol_species <- c("green", "deeppink", "orange", "orange2", "blue2", "red2", "yellow2")
## READS AVERAGE colored by STATUS
eren <- ggplot(metaseq, aes(x = Map_SUM, y = Inputtrim_reads, color = Species, label = SampleID))
eren <- eren + geom_point(size = 2, alpha = 0.7)
eren <- eren + scale_color_manual(values = mycol_species)
eren <- eren + theme_calc()
eren <- eren + geom_hline(yintercept = 3e+07, linetype = "dotted", color = "green3")
eren <- eren + geom_hline(yintercept = 5e+07, linetype = "dotted", color = "green3")
eren <- eren + geom_vline(xintercept = 80, linetype = "dotted", color = "blue2")
eren <- eren + xlim(0, 100)
options(scipen = 20) #to remove the scientific annotation of the axis
## make an interactive version of the scatter plot
attacktitan <- ggplotly(eren)
attacktitanWe added the green thresholds to indicate how many reads are recommended by Illumina (lower end and optimal). The blue line demonstrates where the mapping ratio could be considered not contaminated.
STAR mapping to alternate
species## READS AVERAGE colored by STATUS
mikasa <- ggplot(metaseq, aes(x = Map_SUM, y = Inputtrim_reads, color = Species,
label = SampleID))
mikasa <- mikasa + geom_point(size = 2, alpha = 0.7)
mikasa <- mikasa + scale_color_manual(values = mycol_species)
mikasa <- mikasa + theme_calc()
mikasa <- mikasa + geom_hline(yintercept = 30000000, linetype = "dotted", color = "green3")
mikasa <- mikasa + geom_hline(yintercept = 50000000, linetype = "dotted", color = "green3")
mikasa <- mikasa + geom_vline(xintercept = 80, linetype = "dotted", color = "blue2")
mikasa <- mikasa + xlim(0, 100)
options(scipen = 20) #to remove the scientific annotation of the axis
## make an interactive version of the scatter plot
attacktitan <- ggplotly(eren)
attacktitanWe added the green thresholds to indicate how many reads are recommended by Illumina (lower end and optimal). The blue line demonstrates where the mapping ratio could be considered not contaminated.
sessionInfo()FALSE R version 4.2.1 (2022-06-23)
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