Common sequences plot

Description

Creates a scatter plot of just the sequences in common between two samples.

Usage

commonSeqsPlot(sample1, sample2, productive.aa)

Arguments

Details

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

Value

Returns a frequency scatter plot of two samples showing only the shared sequences.

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")

commonSeqsPlot("TCRB_Day32_Unsorted", "TCRB_Day83_Unsorted", 
   productive.aa = productive.aa)

# Change the X and Y axises to log-10 scale
commonSeqsPlot("TCRB_Day32_Unsorted", "TCRB_Day83_Unsorted", 
   productive.aa = productive.aa) +
   ggplot2::scale_x_log10() + 
   ggplot2::scale_y_log10() + 
   ggplot2::annotation_logticks(sides = "bl")

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)

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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/commonSeqsPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: commonSeqsPlot
> ### Title: Common sequences plot
> ### Aliases: commonSeqsPlot
> 
> ### ** 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%
> 
> commonSeqsPlot("TCRB_Day32_Unsorted", "TCRB_Day83_Unsorted", 
+    productive.aa = productive.aa)
> 
> # Change the X and Y axises to log-10 scale
> commonSeqsPlot("TCRB_Day32_Unsorted", "TCRB_Day83_Unsorted", 
+    productive.aa = productive.aa) +
+    ggplot2::scale_x_log10() + 
+    ggplot2::scale_y_log10() + 
+    ggplot2::annotation_logticks(sides = "bl")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>