library(ggplot2)
library(reshape2)
setwd("/home/chris/hydrogen/scripts/aligner_compare/sorghum")
real_tpm <- read.table("reads.tpm", sep="\t", as.is=T, header=F, colClasses=c("character", "numeric"))
names(real_tpm) <- c("id", "realtpm")
bowtie2 <- read.table("bowtie2/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
bwa <- read.table("bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
snap <- read.table("snap/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
salmonbwa <- read.table("salmon-bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
names(bowtie2) <- c("id", "bowtie2.length", "bowtie2.tpm", "bowtie2.reads")
names(bwa) <- c("id", "bwa.length", "bwa.tpm", "bwa.reads")
names(snap) <- c("id", "snap.length", "snap.tpm", "snap.reads")
names(salmonbwa) <- c("id", "salmonbwa.length", "salmonbwa.tpm", "salmonbwa.reads")
data <- merge(x=real_tpm, y=bowtie2, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=bwa, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=snap, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=salmonbwa, by.x="id", by.y="id", all=T)
data <- data[,c(1,2,4,7,10,13)]
names(data) <- c("id", "real", "bowtie2", "bwa", "snap", "salmonbwa")
mdata <- melt(data, id="id")
ggplot(mdata, aes(x=log(value),colour=variable)) +
geom_density() +
xlim(-4,10) +
ggtitle("sorghum tpm density plot")
ggplot(data, aes(x=log(real), y=log(bowtie2))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bowtie2 vs real tpm")
ggplot(data, aes(x=log(real), y=log(bwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bwa vs real tpm")
ggplot(data, aes(x=log(real), y=log(snap))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("snap vs real tpm")
ggplot(data, aes(x=log(real), y=log(salmonbwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("salmon-bwa vs real tpm")
error <- data.frame((data$real - data$bwa)^2)
error$bowtie2_error <- (data$real - data$bowtie2)^2
error$snap_error <- (data$real - data$snap)^2
error$salmonbwa_error <- (data$real - data$salmonbwa)^2
names(error) <- c("bwa_error", "bowtie2_error", "snap_error", "salmon-bwa_error")
df <- data.frame(colSums(x=error))
apply(df,1,sqrt)
## bwa_error bowtie2_error snap_error salmon-bwa_error
## 14112.11786 5068.97560 3896.95416 95.25991
setwd("/home/chris/hydrogen/scripts/aligner_compare/rice")
real_tpm <- read.table("reads.tpm", sep="\t", as.is=T, header=F, colClasses=c("character", "numeric"))
names(real_tpm) <- c("id", "realtpm")
bowtie2 <- read.table("bowtie2/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
bwa <- read.table("bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
snap <- read.table("snap/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
salmonbwa <- read.table("salmon-bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
names(bowtie2) <- c("id", "bowtie2.length", "bowtie2.tpm", "bowtie2.reads")
names(bwa) <- c("id", "bwa.length", "bwa.tpm", "bwa.reads")
names(snap) <- c("id", "snap.length", "snap.tpm", "snap.reads")
names(salmonbwa) <- c("id", "salmonbwa.length", "salmonbwa.tpm", "salmonbwa.reads")
data <- merge(x=real_tpm, y=bowtie2, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=bwa, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=snap, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=salmonbwa, by.x="id", by.y="id", all=T)
data <- data[,c(1,2,4,7,10,13)]
names(data) <- c("id", "real", "bowtie2", "bwa", "snap", "salmonbwa")
mdata <- melt(data, id="id")
ggplot(mdata, aes(x=log(value),colour=variable)) +
geom_density() +
xlim(-4,10) +
ggtitle("rice tpm density plot")
ggplot(data, aes(x=log(real), y=log(bowtie2))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bowtie2 vs real tpm")
ggplot(data, aes(x=log(real), y=log(bwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bwa vs real tpm")
ggplot(data, aes(x=log(real), y=log(snap))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("snap vs real tpm")
ggplot(data, aes(x=log(real), y=log(salmonbwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("salmon-bwa vs real tpm")
error <- data.frame((data$real - data$bwa)^2)
error$bowtie2_error <- (data$real - data$bowtie2)^2
error$snap_error <- (data$real - data$snap)^2
error$salmonbwa_error <- (data$real - data$salmonbwa)^2
names(error) <- c("bwa_error", "bowtie2_error", "snap_error", "salmon-bwa_error")
df <- data.frame(colSums(x=error))
apply(df,1,sqrt)
## bwa_error bowtie2_error snap_error salmon-bwa_error
## 17153.957 6491.273 9493.125 1567.724
setwd("/home/chris/hydrogen/scripts/aligner_compare/mouse")
real_tpm <- read.table("reads.tpm", sep="\t", as.is=T, header=F, colClasses=c("character", "numeric"))
names(real_tpm) <- c("id", "realtpm")
bowtie2 <- read.table("bowtie2/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
bwa <- read.table("bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
snap <- read.table("snap/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
salmonbwa <- read.table("salmon-bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
names(bowtie2) <- c("id", "bowtie2.length", "bowtie2.tpm", "bowtie2.reads")
names(bwa) <- c("id", "bwa.length", "bwa.tpm", "bwa.reads")
names(snap) <- c("id", "snap.length", "snap.tpm", "snap.reads")
names(salmonbwa) <- c("id", "salmonbwa.length", "salmonbwa.tpm", "salmonbwa.reads")
data <- merge(x=real_tpm, y=bowtie2, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=bwa, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=snap, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=salmonbwa, by.x="id", by.y="id", all=T)
data <- data[,c(1,2,4,7,10,13)]
names(data) <- c("id", "real", "bowtie2", "bwa", "snap", "salmonbwa")
mdata <- melt(data, id="id")
ggplot(mdata, aes(x=log(value),colour=variable)) +
geom_density() +
xlim(-4,10) +
ggtitle("mouse tpm density plot")
ggplot(data, aes(x=log(real), y=log(bowtie2))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bowtie2 vs real tpm")
ggplot(data, aes(x=log(real), y=log(bwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bwa vs real tpm")
ggplot(data, aes(x=log(real), y=log(snap))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("snap vs real tpm")
ggplot(data, aes(x=log(real), y=log(salmonbwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("salmon-bwa vs real tpm")
error <- data.frame((data$real - data$bwa)^2)
error$bowtie2_error <- (data$real - data$bowtie2)^2
error$snap_error <- (data$real - data$snap)^2
error$salmonbwa_error <- (data$real - data$salmonbwa)^2
names(error) <- c("bwa_error", "bowtie2_error", "snap_error", "salmon-bwa_error")
df <- data.frame(colSums(x=error))
apply(df,1,sqrt)
## bwa_error bowtie2_error snap_error salmon-bwa_error
## 18108.409 7208.840 13313.957 3041.594
setwd("/home/chris/hydrogen/scripts/aligner_compare/yeast")
real_tpm <- read.table("reads.tpm", sep="\t", as.is=T, header=F, colClasses=c("character", "numeric"))
names(real_tpm) <- c("id", "realtpm")
bowtie2 <- read.table("bowtie2/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
bwa <- read.table("bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
snap <- read.table("snap/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
salmonbwa <- read.table("salmon-bwa/quant.sf", sep="\t", header=F, colClasses=c("character","numeric","numeric","numeric"))
names(bowtie2) <- c("id", "bowtie2.length", "bowtie2.tpm", "bowtie2.reads")
names(bwa) <- c("id", "bwa.length", "bwa.tpm", "bwa.reads")
names(snap) <- c("id", "snap.length", "snap.tpm", "snap.reads")
names(salmonbwa) <- c("id", "salmonbwa.length", "salmonbwa.tpm", "salmonbwa.reads")
data <- merge(x=real_tpm, y=bowtie2, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=bwa, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=snap, by.x="id", by.y="id", all=T)
data <- merge(x=data, y=salmonbwa, by.x="id", by.y="id", all=T)
data <- data[,c(1,2,4,7,10,13)]
names(data) <- c("id", "real", "bowtie2", "bwa", "snap", "salmonbwa")
mdata <- melt(data, id="id")
ggplot(mdata, aes(x=log(value),colour=variable)) +
geom_density() +
xlim(-4,10) +
ggtitle("sorghum tpm density plot")
ggplot(data, aes(x=log(real), y=log(bowtie2))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bowtie2 vs real tpm")
ggplot(data, aes(x=log(real), y=log(bwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("bwa vs real tpm")
ggplot(data, aes(x=log(real), y=log(snap))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("snap vs real tpm")
ggplot(data, aes(x=log(real), y=log(salmonbwa))) +
geom_point(alpha=0.1) +
xlim(-1,10) +
ylim(-1,10) +
ggtitle("salmon-bwa vs real tpm")
error <- data.frame((data$real - data$bwa)^2)
error$bowtie2_error <- (data$real - data$bowtie2)^2
error$snap_error <- (data$real - data$snap)^2
error$salmonbwa_error <- (data$real - data$salmonbwa)^2
names(error) <- c("bwa_error", "bowtie2_error", "snap_error", "salmon-bwa_error")
df <- data.frame(colSums(x=error))
apply(df,1,sqrt)
## bwa_error bowtie2_error snap_error salmon-bwa_error
## 22661.60 27646.82 21136.79 16155.67
#library(markdown)
#setwd("/home/chris/hydrogen/scripts/aligner_compare/")
#result <- rpubsUpload("Aligner Comparison", "compare.html")
#if (!is.null(result$continueUrl))
# browseURL(result$continueUrl) else stop(result$error)