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| Package: CancerEvolutionVisualization | ||
| Title: Publication Quality Phylogenetic Tree Plots | ||
| Version: 2.1.0 | ||
| Date: 2024-07-19 | ||
| Date: 2024-07-31 | ||
| Authors@R: c( | ||
| person("Paul Boutros", role = "cre", email = "[email protected]"), | ||
| person("Adriana Salcedo", role = "aut"), | ||
|
|
||
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| \docType{data} | ||
| \name{GRCh37} | ||
| \alias{GRCh37} | ||
| \title{GRCh37 Chromosom Information} | ||
| \description{Chromosome information for the GRCh37 genome build. Used for plotting.} | ||
| \format{data.frame} |
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| \docType{data} | ||
| \name{GRCh38} | ||
| \alias{GRCh38} | ||
| \title{GRCh38 Chromosom Information} | ||
| \description{Chromosome information for the GRCh38 genome build. Used for plotting.} | ||
| \format{data.frame} |
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| \name{create.ccf.heatmap} | ||
| \alias{create.ccf.heatmap} | ||
| \title{Subclone Tree Plot} | ||
| \description{ | ||
| Creates a heatmap of cancer cell fraction (CCF) distribution across tumour samples. The function is a wrapper around \code{BoutrosLab.plotting.general::create.heatmap()} with some changes in the default parameters. All parameter description are the same as in \code{BoutrosLab.plotting.general::create.heatmap()} except for \code{ccf.thres}. | ||
| } | ||
| \usage{ | ||
| create.ccf.heatmap( | ||
| x, | ||
| ccf.thres = NULL, | ||
| cluster.dimensions = 'both', | ||
| clustering.method = 'complete', | ||
| distance.method = 'euclidean', | ||
| xaxis.lab = '', | ||
| xlab.label = 'Mutations', | ||
| print.colour.key = FALSE, | ||
| colour.scheme = c('white', 'blue'), | ||
| ... | ||
| ) | ||
| } | ||
| \arguments{ | ||
| \item{x}{Either a data-frame or a matrix from which the heatmap is to created} | ||
| \item{ccf.thres}{CCF threshold to be applied to the heatmap. Values below the threshold will be set to 0. Defaults to \code{NULL}} | ||
| \item{cluster.dimensions}{Defaults to \dQuote{both}.} | ||
| \item{clustering.method}{Defaults to \dQuote{complete}.} | ||
| \item{distance.method}{Defaults to \dQuote{euclidean}.} | ||
| \item{xaxis.lab}{Defaults to an empty string.} | ||
| \item{xlab.label}{Defaults to \dQuote{Mutations}.} | ||
| \item{print.colour.key}{Defaults to \code{FALSE}.} | ||
| \item{colour.scheme}{Defaults to \code{c('white', 'blue')}.} | ||
| \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.} | ||
| } | ||
| \value{A `grob` object of the heatmap.} | ||
| \author{Helena Winata} |
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| \name{create.ccf.summary.heatmap} | ||
| \alias{create.ccf.summary.heatmap} | ||
| \title{Subclone Tree Plot} | ||
| \description{ | ||
| Creates a heatmap of cancer cell fraction (CCF) distribution across tumour samples with clone IDs as a covariate beneath the heatmap. Subplot parameters controls the appearance of the heatmap and barplots. See \code{BoutrosLab.plotting.general::create.barplot()} or \code{BoutrosLab.plotting.general::create.heatmap()} for parameter description. Legend parameters are passed to \code{BoutrosLab.plotting.general::legend.grob()}. | ||
| } | ||
|
|
||
| \usage{ | ||
| create.ccf.summary.heatmap( | ||
| DF, | ||
| ccf.thres = NULL, | ||
| median.col = 'median.ccf.per.sample', | ||
| clone.order = NULL, | ||
| sample.order = NULL, | ||
| hm.col.scheme = c('white', 'blue'), | ||
| subplot.xlab.cex = 1.2, | ||
| subplot.xaxis.cex = 1, | ||
| subplot.xaxis.fontface = 'bold', | ||
| subplot.xaxis.rot = 90, | ||
| subplot.ylab.cex = 1.2, | ||
| subplot.yaxis.cex = 1, | ||
| subplot.yaxis.fontface = 'bold', | ||
| hm.xaxis.rot = 90, | ||
| legend.size = 3, | ||
| legend.title.cex = 1.2, | ||
| legend.label.cex = 1, | ||
| ... | ||
| ); | ||
| } | ||
| \arguments{ | ||
| \item{DF}{A data-frame with the following column names: 'ID', 'SNV.id', 'clone.id', 'CCF'.} | ||
| \item{ccf.thres}{CCF threshold to be applied to the heatmap. Values below the threshold will be set to 0. Defaults to \code{NULL}} | ||
| \item{median.col}{Defaults to \dQuote{median.ccf.per.sample}} | ||
| \item{clone.order}{Defaults to \code{NULL}} | ||
| \item{sample.order}{Defaults to \code{NULL}} | ||
| \item{hm.col.scheme}{Heatmap colour scheme. Defaults to \code{c('white', 'blue')}} | ||
| \item{subplot.xlab.cex}{Subplot parameter. Defaults to 1.2} | ||
| \item{subplot.xaxis.cex}{Subplot parameter. Defaults to 1} | ||
| \item{subplot.xaxis.fontface}{Subplot parameter. Defaults to \dQuote{bold}} | ||
| \item{subplot.xaxis.rot}{Subplot parameter. Defaults to 90} | ||
| \item{subplot.ylab.cex}{Subplot parameter. Defaults to 1.2} | ||
| \item{subplot.yaxis.cex}{Subplot parameter. Defaults to 1} | ||
| \item{subplot.yaxis.fontface}{Subplot parameter. Defaults to \dQuote{bold}} | ||
| \item{hm.xaxis.rot}{Subplot parameter. Defaults to 90} | ||
| \item{legend.size}{Legend parameter. Defaults to 3} | ||
| \item{legend.title.cex}{Legend parameter. Defaults to 1.2} | ||
| \item{legend.label.cex}{Legend parameter. Defaults to 1} | ||
| \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.multipanelplot() for further details.} | ||
|
|
||
| } | ||
| \value{A `grob` object of the summary plot.} | ||
| \author{Helena Winata} |
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| \name{create.clone.genome.distribution.plot} | ||
| \alias{create.clone.genome.distribution.plot} | ||
| \title{Create Clone Genome Distribution Plot} | ||
| \description{ | ||
| This function creates a plot showing the distribution of clones across the genome. It generates a scatter plot of the SNVs colored by clone ID and a density plot showing the density of each clone across the genome. The function can handle both single and multi-sample inputs. | ||
| } | ||
| \usage{ | ||
| create.clone.genome.distribution.plot( | ||
| snv.df, | ||
| genome.build = 'GRCh37', | ||
| clone.order = NULL, | ||
| clone.colours = NULL, | ||
| filename = NULL, | ||
| multi.sample = FALSE, | ||
| ... | ||
| ) | ||
| } | ||
| \arguments{ | ||
| \item{snv.df}{A data frame containing the SNV data. It must have columns 'chr', 'pos', and 'clone.id'. If \code{multi.sample = TRUE}, it must also have a column 'ID' specifying the sample ID for each SNV.} | ||
| \item{genome.build}{The genome build to use. Defaults to \dQuote{GRCh37}.} | ||
| \item{clone.order}{The order in which to plot the clones. If \code{NULL}, clones will be sorted alphabetically.} | ||
| \item{clone.colours}{A named vector specifying the color to use for each clone. If \code{NULL}, colors will be automatically assigned.} | ||
| \item{filename}{Directory or filepath to save the plot in. If \code{multi.sample = TRUE}, this must be a directory. if \code{multi.sample = FALSE}, this must be a filepath. If \code{NULL}, the plot will not be saved.} | ||
| \item{multi.sample}{Logical indicating whether the input data contains multiple samples. Defaults to \code{FALSE}.} | ||
| \item{...}{Additional arguments to be passed to \code{BoutrosLab.plotting.general::create.multipanelplot()}.} | ||
| } | ||
| \details{ | ||
| This function preprocesses the input data frame, extracts chromosome information, and iterates over each sample to create a clone genome distribution plot. For each sample, it calculates the density of each clone across the genome and creates a scatter plot of the SNVs colored by clone ID and a density plot showing the density of each clone. | ||
| } | ||
| \value{A `grob` object.} | ||
| \author{Helena Winata, Selina Wu} | ||
|
|
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