plotHist: Plot histogram of clonotype frequencies in negative and...

In BioHPC/iCAT: immune Cell Analysis Tool

Description

Plot histogram of clonotype frequencies in negative and positive samples.

Usage

plotHist(comb)

Arguments

comb	List containing both negtive (n) and positive (v) clonotype percentages.

Value

ggplot histogram of clonotype frequencies in negative and positive samples

Examples

FIELD <- "vGeneName aminoAcid jGeneName"
COUNT <- "copy"
P_CUTOFF <- 0.1
MIN_PUBLIC <- 2
COPY_RANGE <- "1 99"

listPos <- tsvDir(system.file("extdata", "Post", package="iCAT"))
listNeg <- tsvDir(system.file("extdata", "Pre", package="iCAT"))

naive <- readTrn(listNeg, FIELD, COUNT, COPY_RANGE, "naive")
vaccs <- readTrn(listPos, FIELD, COUNT, COPY_RANGE, "vacc")  

mod <- train(naive, vaccs, listNeg, listPos, FIELD, COUNT, COPY_RANGE, P_CUTOFF, MIN_PUBLIC, NULL)
plotHist(mod)

BioHPC/iCAT documentation built on Oct. 30, 2021, 3:12 p.m.