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.Rhistory
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ret
mapping.orig <- read.delim("~/Dropbox/UMN/KnightsLab/MLRepo/datasets/sokol/mapping-orig.txt", quote="")
View(mapping.orig)
tasks <- read.delim("~/Dropbox/UMN/KnightsLab/MLRepo/tasks.txt", quote="")
View(tasks)
mapping.orig <- read.delim("~/Dropbox/UMN/KnightsLab/MLRepo/datasets/karlsson/mapping-orig.txt", quote="")
View(mapping.orig)
mapping.orig <- read.delim("~/Dropbox/UMN/KnightsLab/MLRepo/datasets/karlsson/mapping-orig.txt", quote="", stringsAsFactors=FALSE)
View(mapping.orig)
otutable <- read.delim("~/Dropbox/UMN/KnightsLab/MLRepo/datasets/karlsson/otutable.txt", quote="", stringsAsFactors=FALSE)
View(otutable)
datadirname <- "denovo"
setwd("/Users/pvangay/Dropbox/UMN/KnightsLab/IMP/ANALYSES/analysis")
source("bin/load.r")
map_L <- map[map$Sub.Study == "L",]
# IMP.049 and IMP.050 were recruited at 2 months and 3 months respectively - these might be throwing things off
map_L <- map_L[!(map_L$Subject.ID %in% c("IMP.049", "IMP.050")),]
debugSource('~/Dropbox/UMN/KnightsLab/IMP/ANALYSES/analysis/lib/b.p.ratio.r')
plot.b.p.ratio(map_L, taxa, bug1=bacteroides, bug2=prevotella, outputfn="b.p.ratio.L.1.6.pdf", longitudinal=T, num.clip.months=1)
View(mins)
View(mean.d)
debugSource('~/Dropbox/UMN/KnightsLab/IMP/ANALYSES/analysis/lib/b.p.ratio.r')
plot.b.p.ratio(map_L, taxa, bug1=bacteroides, bug2=prevotella, outputfn="b.p.ratio.L.1.6.pdf", longitudinal=T, num.clip.months=1)
direction
this.data[this.data$x == "end", "bp"] - this.data[this.data$x == "start", "bp"]
debugSource('~/Dropbox/UMN/KnightsLab/IMP/ANALYSES/analysis/lib/b.p.ratio.r')
debugSource('~/Dropbox/UMN/KnightsLab/IMP/ANALYSES/analysis/lib/b.p.ratio.r')
plot.b.p.ratio(map_L, taxa, bug1=bacteroides, bug2=prevotella, outputfn="b.p.ratio.L.1.6.pdf", longitudinal=T, num.clip.months=1)