In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = TRUE)
library(plotly)
library(magrittr)

Started on r format(Sys.time(), "%Y-%m-%d %H:%M:%S")

VcfStats_Result {.tabset}

Number of SNPs

data <- read.table(snp_counts, sep="\t", skip=2)
names(data) <- c("Counts", "Sample")
samples <- gsub("samples/", "", data$Sample)
plot_ly(data, x = samples, y = data$Counts)

Private/Shared SNPs

data <- read.table(private_snp_counts, sep="\t", skip=1)
names(data) <- c("Private_SNPs", "Sample")
fig <- plot_ly(data, x = ~Sample, y = ~Private_SNPs, type = 'bar', name = 'Private SNPs')
fig <- fig %>% layout(title = 'Private SNPs', yaxis = list(title = 'Count'), xaxis=list(title=''))
fig

data <- read.table(shared_snp_counts, sep="\t", skip=1)
names(data) <- c("Shared_SNPs", "Count")
fig <- plot_ly(data, x = ~Shared_SNPs, y = ~Count, type = 'bar', name = 'Shared SNPs')
fig <- fig %>% layout(title = 'Shared SNPs', yaxis = list(title = 'Count'), xaxis=list(title='Number of shared SNPs'))
fig

Transisions/Transversions

data <- read.table(tstv, sep="\t", skip=1)
names(data) <- c("Transisions", "Transversions", "tstv", "Sample")
fig <- plot_ly(data, x = ~Sample, y = ~tstv, type = 'bar', name = 'Transisions/Transversions')
fig <- fig %>% layout(yaxis = list(title = 'ts/tv'), xaxis=list(title=''))
fig

Input Dataset

ezInteractiveTableRmd(values=ans4Report[["dataset"]])

SessionInfo

ezSessionInfo()

uzh/ezRun documentation built on May 4, 2024, 3:23 p.m.