Last data update: 2014.03.03

 R: Clone tracking plot
cloneTrackR Documentation

Clone tracking plot

Description

Creates line plot tracking amino acid frequencies across multiple samples

Usage

cloneTrack(sequence.matrix, map = "none", productive.aa, label = "none",
  track = "none", unassigned = TRUE)

Arguments

sequence.matrix

A sequence matrix generated from the LymphoSeq function seqMatrix.

map

An optional character vector of one or more sample names contained in the productive.aa list. If the same sequence appears in multiple mapped samples, then it will be assigned the label of the first listed sample only.

productive.aa

A list of data frames of productive amino acid sequences containing the samples to be mapped. This parameter is only required if sequence mapping is performed.

label

An optional character vector of one or more labels used to annotate the mapped sequences. The order of the labels must match the order of the samples listed in map.

track

An optional character vector of one or more amino acid sequences to track.

unassigned

A Boolean value indicating whether or not to draw the lines of sequences not being mapped or tracked. If TRUE then the unassigned sequences are drawn. If FALSE, then the unassigned sequences are not drawn.

Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

Value

Returns a line plot showing the amino acid frequencies across multiple samples in the sequence matrix where each line represents one unique sequence.

See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/).

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

top.freq <- topFreq(productive.aa = productive.aa, percent = 0.1)

sequence.matrix <- seqMatrix(productive.aa = productive.aa, sequences = top.freq$aminoAcid)

# Track clones without mapping or tracking specific sequences
cloneTrack(sequence.matrix = sequence.matrix)

# Track top 20 clones mapping to the CD4 and CD8 samples
cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
   map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
   track = top.freq$aminoAcid[1:20], unassigned = TRUE) 

# Track the top 10 clones from top.freq
cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
   track = top.freq$aminoAcid[1:10], unassigned = FALSE) 

# Track clones mapping to the CD4 and CD8 samples while ignoring all others
cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
   map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
   unassigned = FALSE) 

# Track clones mapping to the CD4 and CD8 samples and track 2 specific sequences
cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
   map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
   track = c("CASSPPTGERDTQYF", "CASSQDRTGQYGYTF"), unassigned = FALSE)

# Reorder the x axis, change the axis labels, convert to log scale, and add title
x.limits <- c("TCRB_Day0_Unsorted", "TCRB_Day32_Unsorted", 
   "TCRB_Day83_Unsorted", "TCRB_Day949_Unsorted", "TCRB_Day1320_Unsorted")

sequence.matrix <- sequence.matrix[ ,c("aminoAcid", x.limits)]
   
clone.track <- cloneTrack(sequence.matrix = sequence.matrix, 
   productive.aa = productive.aa, track = top.freq$aminoAcid[1:10], unassigned = FALSE) 

x.labels <- c("Day 0", "Day 32", "Day 83", "Day 949", "Day 1320")

clone.track + 
   ggplot2::scale_x_discrete(expand = c(0,0), labels = x.labels) + 
   ggplot2::scale_y_log10() + ggplot2::annotation_logticks(sides = "l") + 
   ggplot2::ggtitle("Figure Title")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/cloneTrack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cloneTrack
> ### Title: Clone tracking plot
> ### Aliases: cloneTrack
> 
> ### ** Examples
> 
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
> 
> file.list <- readImmunoSeq(path = file.path)
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> top.freq <- topFreq(productive.aa = productive.aa, percent = 0.1)
> 
> sequence.matrix <- seqMatrix(productive.aa = productive.aa, sequences = top.freq$aminoAcid)
> 
> # Track clones without mapping or tracking specific sequences
> cloneTrack(sequence.matrix = sequence.matrix)
> 
> # Track top 20 clones mapping to the CD4 and CD8 samples
> cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
+    map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
+    track = top.freq$aminoAcid[1:20], unassigned = TRUE) 
> 
> # Track the top 10 clones from top.freq
> cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
+    track = top.freq$aminoAcid[1:10], unassigned = FALSE) 
> 
> # Track clones mapping to the CD4 and CD8 samples while ignoring all others
> cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
+    map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
+    unassigned = FALSE) 
> 
> # Track clones mapping to the CD4 and CD8 samples and track 2 specific sequences
> cloneTrack(sequence.matrix = sequence.matrix, productive.aa = productive.aa, 
+    map = c("TCRB_Day949_CD4", "TCRB_Day949_CD8"), label = c("CD4", "CD8"), 
+    track = c("CASSPPTGERDTQYF", "CASSQDRTGQYGYTF"), unassigned = FALSE)
> 
> # Reorder the x axis, change the axis labels, convert to log scale, and add title
> x.limits <- c("TCRB_Day0_Unsorted", "TCRB_Day32_Unsorted", 
+    "TCRB_Day83_Unsorted", "TCRB_Day949_Unsorted", "TCRB_Day1320_Unsorted")
> 
> sequence.matrix <- sequence.matrix[ ,c("aminoAcid", x.limits)]
>    
> clone.track <- cloneTrack(sequence.matrix = sequence.matrix, 
+    productive.aa = productive.aa, track = top.freq$aminoAcid[1:10], unassigned = FALSE) 
> 
> x.labels <- c("Day 0", "Day 32", "Day 83", "Day 949", "Day 1320")
> 
> clone.track + 
+    ggplot2::scale_x_discrete(expand = c(0,0), labels = x.labels) + 
+    ggplot2::scale_y_log10() + ggplot2::annotation_logticks(sides = "l") + 
+    ggplot2::ggtitle("Figure Title")
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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