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).