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Last data update: 2014.03.03

R: Construct transition-transversion plot

TvTi	R Documentation

Construct transition-transversion plot

Description

Given a data frame construct a plot displaying the proportion or frequency of transition and transversion types observed in a cohort.

Usage

TvTi(x, fileType = NULL, y = NULL, clinData = NULL, type = "Proportion",
  lab_Xaxis = TRUE, lab_txtAngle = 45, palette = c("#D53E4F", "#FC8D59",
  "#FEE08B", "#E6F598", "#99D594", "#3288BD"), tvtiLayer = NULL,
  expecLayer = NULL, sort = "none", clinLegCol = NULL,
  clinVarCol = NULL, clinVarOrder = NULL, clinLayer = NULL,
  progress = TRUE, out = "plot")

Arguments

`x`	Object of class data frame with rows representing transitions and transversions. The data frame must contain the following columns 'sample', reference' and 'variant' or alternatively "Tumor_Sample_Barcode", "Reference_Allele", "Tumor_Seq_Allele1", "Tumor_Seq_Allele2" depending on the argument supplied to the fileType parameter. (required)
`fileType`	Character string specifying the format the input given to parameter x is in, one of 'MAF', 'MGI'. The former option requires the data frame given to x to contain the following column names "Tumor_Sample_Barcode", "Reference_Allele", "Tumor_Seq_Allele1", "Tumor_Seq_Allele2" the later option requires the data frame givin to x to contain the following column names "reference", "variant" and "sample". (required)
`y`	Named vector or data frame representing the expected transition and transversion rates. Either option must name transition and transverions as follows: "A->C or T->G (TV)", "A->G or T->C (TI)", "A->T or T->A (TV)", "G->A or C->T (TI)", "G->C or C->G (TV)", "G->T or C->A (TV)". If specifying a data frame, the data frame must contain the following columns names "Prop", "trans_tranv" (optional see vignette).
`clinData`	Object of class data frame with rows representing clinical data. The data frame should be in "long format" and columns must be names as "sample", "variable", and "value" (optional see details and vignette).
`type`	Character string specifying if the plot should display the Proportion or Frequency of transitions/transversions observed. One of "Proportion" or "Frequency", defaults to "Proportion".
`lab_Xaxis`	Boolean specifying whether to label the x-axis in the plot.
`lab_txtAngle`	Integer specifying the angle of labels on the x-axis of the plot.
`palette`	Character vector of length 6 specifying colours for each of the six possible transition transversion types.
`tvtiLayer`	Valid ggplot2 layer to be added to the main plot.
`expecLayer`	Valid ggplot2 layer to be added to the expected sub-plot.
`sort`	Character string specifying the sort order of the sample variables in the plot. Arguments to this parameter should be "sample", "tvti", or "none" to sort the x-axis by sample name, transition transversion frequency, or no sort respectively.
`clinLegCol`	Integer specifying the number of columns in the legend for the clinical data, only valid if argument is supplied to parameter clinData.
`clinVarCol`	Named character vector specifying the mapping of colours to variables in the variable column of the data frame supplied to clinData (ex. "variable"="colour").
`clinVarOrder`	Character vector specifying the order in which to plot variables in the variable column of the argument given to the parameter clinData. The argument supplied to this parameter should have the same unique length and values as in the variable column of the argument supplied to parameter clinData (see vignette).
`clinLayer`	Valid ggplot2 layer to be added to the clinical sub-plot.
`progress`	Boolean specifying if progress bar should be displayed for the function.
`out`	Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Details

TvTi is a function designed to display proportion or frequency of transitions and transversion seen in a data frame supplied to parameter x.

Value

One of the following, a list of dataframes containing data to be plotted, a grob object, or a plot.

Examples

TvTi(brcaMAF, type='Frequency',
palette=c("#77C55D", "#A461B4", "#C1524B", "#93B5BB", "#4F433F", "#BFA753"),
lab_txtAngle=60, fileType="MAF")

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(GenVisR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenVisR/TvTi.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TvTi
> ### Title: Construct transition-transversion plot
> ### Aliases: TvTi
> 
> ### ** Examples
> 
> TvTi(brcaMAF, type='Frequency',
+ palette=c("#77C55D", "#A461B4", "#C1524B", "#93B5BB", "#4F433F", "#BFA753"),
+ lab_txtAngle=60, fileType="MAF")
Found appropriate columns
Removed 209 indels present in data
annotating transitions and transversions
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Warning message:
In TvTi_rmMnuc(x) :
  Multi Nucleotide codes are not currently supported, removed: 2 multi-nucleotides present in the data
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>