TvTi: Construct transition-transversion plot

Description Usage Arguments Details Value Examples

View source: R/TvTi.R

Description

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

Usage

1
2
3
4
5
6
7
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", sample_order_input, layers = NULL,
  return_plot = FALSE)

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).

sample_order_input

Sample orders to be used

layers

ggplot object to be added to proportions plot

return_plot

Return as ggplot object? Only returns main plot

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

1
2
3
TvTi(brcaMAF, type='Frequency',
palette=c("#77C55D", "#A461B4", "#C1524B", "#93B5BB", "#4F433F", "#BFA753"),
lab_txtAngle=60, fileType="MAF")

GenVisR documentation built on Nov. 17, 2017, 10:41 a.m.