TvTi: Construct transition-transversion plot

In griffithlab/GenVisR: Genomic Visualizations in R

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",
  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

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

griffithlab/GenVisR documentation built on May 14, 2024, 12:40 a.m.