plot.variant.clusters: Plot variant clustering using combination of box, violin, and...
In hdng/clonevol: Clonal ordering and visualization

Description Usage Arguments Examples

Plot variant clustering using combination of box, violin, and jitter plots. Value in columns vaf.col.names variants data.frame, grouped group by cluster.col.name column

1	variant.box.plot(df, cluster.col.name, vaf.col.names, ...)

`df`	Variants data frame, containing at least 'cluster' and VAF or CCF columns
`cluster.col.name`	Name of cluster column in df (default='cluster')
`vaf.col.names`	Names of VAF columns in df
`panel.border.colors`	Colors of panel.border of sample plot
`panel.border.sizes`	Line sizes of panel.border of sample plot
`panel.border.linetypes`	Line types of panel.border of sample plot
`vaf.suffix`	Suffix to add to vaf.col.names and display in plot axis
`vaf.limits`	Vector (or scalar) of max VAF in
`variant.class.col.name`	Name of the column containing classification of variants
`show.cluster.size`	show cluster size in the box, jitter, violin plots
`cluster.size.text.color`	Cluster size text color (default='blue')
`cluster.axis.name`	Name to place before cluster IDs in the cluster axis (default = 'cluster:')
`show.cluster.axis.label`	Show label of the cluster axis (deafault=TRUE)
`sample.title.size`	Text size of the label of the sample axis (default defined relative to param base_size)
`cluster.title.size`	Text size of the label of the cluster axis (default defined relative to param base_size)
`base_size`	base_size Paramter to passed to in ggplot2 theme_bw(base_size)
`width, height, w1, h1`	(w/h = with/height of whole plot, w1/h1 = width/height of component plot) w1/h1 will orverwite w/h if they are non-zero. If all w/h/w1/h1 are zero (default), auto scale the plots
`axis.ticks.length`	Length of the axes' ticks (default=1)
`axis.text.angle`	Angle of the text used to annotate data points (default=0)
`plot.margin`	Margin of the individual sample plot (default=0.1)
`horizontal`	if TRUE, samples are laid out horizontally, otherwise vertically
`box`	Plot the box plot (default = TRUE)
`box.line.type`	Linetype of the boxplot (eg. 'solid', 'dotted',...)
`box.line.size`	Size of the border/line of the boxplot (default=0.5)
`box.outlier.shape`	Shape of outliers of boxplot (default=1)
`box.alpha`	Alpha (transparency) level of the box (default=0.5)
`violin`	Plot violin plot (default=TRUE)
`violin.line.type`	Line type for violin plot (default='dotted')
`violin.line.size`	Linesize for violin plot (default=0.5)
`violin.fill.color`	Fill color for violin plot (default='grey80')
`violin.alpha`	Alpha (transparency) level of the violin (default=0.5)
`jitter`	Plot jitter plot (default=FALSE)
`jitter.width`	Width of the jitter plot (default=0.5)
`jitter.color`	Jitter color (default='lightblue')
`jitter.alpha`	Alpha level of jitter points (default=0.5)
`jitter.size`	Size of jitter points (default=1)
`jitter.shape`	Shape of jitter points (default=3)
`jitter.center.method`	Method to calculate the center of jitter plot (default='median', can also be 'median')
`jitter.center.color`	Color of the line placed an the center of the jitter plot (default='black')
`jitter.center.size`	Size of the jitter center line (default=1)
`jitter.center.linetype`	Line type of the jitter center line (default='solid')
`jitter.center.display.value`	String indicating the value to show at the center of the jitter points (default='none', can also be 'mean', 'median')
`jitter.center.display.value.text.size`	Size of text showing jitter center value (default=5)
`highlight`	A TRUE/FALSE index vector of the variants in df to higlight and plot using a different color (default=NULL)
`highlight.color`	Color of the higlighted variants in jitter (default='darkgray')
`highlight.fill.color`	Fill color of the jitter points (default='red'), only highlight.shape a is fillable R shape
`highlight.shape`	Shape of the highlighted variant jitter points (default=21)
`highlight.size`	Size of the highligted variant jitter points (default=1)
`highlight.color.col.name`	Name of a column of colors used to highlight the border of the variant points, to be used when we want to highlight different driver variants using different colors, eg. APC by red, TP53 variants by orange, etc. (default=NULL)
`highlight.fill.col.names`	Names of columns that store the values to be filled in variant jitter points (when its R shape is fillable). An example case is to fill points with copy number values stored in highlight.fill.col.names for in individual samples. The length(highlight.fill.col.names) must be equal length(vaf.col.names). (default=NULL).
`highlight.fill.min`	Lower bound of fill value highlight.fill.col.names for gradient fill. Any value lower than this will be fill using the same color (default=1)
`highlight.fill.mid`	Center value in highlight.fill.col.names columns for generating fill gradient (default=2)
`highlight.fill.max`	Higher bound of fill value highlight.fill.col.names for gradient fill. Any value higher than this will be fill using the same color (default=3)
`highlight.fill.min.color`	Low value fill color (default='green'), used in colorpanel(low, mid, hi)
`highlight.fill.mid.color`	Median value fill color (default='black'), used in colorpanel(low, mid, hi)
`highlight.fill.max.color`	High value fill color (default='red'), used in colorpanel(low, mid, hi)
`highlight.size.names`	Column names of the value to be used to scale the size of the variant jitters (default=NULL). Example use case is to draw variants with higher depth bigger.
`max.highlight.size.value`	Max value to provide to size scaling, higher than this does not make the size bigger (default=500)
`size.breaks`	Values used to break sizes to show in legends (default=NULL)
`highlight.size.legend.title`	Title of the size legend (default='depth')
`highlight.note.col.name`	Column name of the label of the highligthed variants (default=NULL), can use gene name, variant details, etc.
`highlight.note.color`	Color used for highligted note (default='blue')
`highlight.note.size`	Size of highlighted note text (default= 3)
`ordered.x`	The order that the clusters are plot (default=NULL)
`order.by.total.vaf`	Order clusters by their total VAF across samples (default=TRUE)
`display.plot`	Show plot (default=TRUE)
`ccf`	Plot CCF (calculated as 2xVAF) instead of VAF (default=FALSE)
`founding.cluster`	Founding cluster (default=NULL)
`show.cluster.label`	Show cluster label in axis (set to FALSE to get more space when too many samples are aligned)
`jitter.center.display.value:`	display cluster center value in the box when show.cluster.size == FALSE
`jitter.center.display.value.text.size:`	text size of the value annotated for the center of the box, jitter, violin plots
`show.cluster.size`	Show cluster size (default=FALSE)
`show.cluster.label`	Show cluster label in axis (default=TRUE)

data(aml1)
pp <- plot.variant.clusters(aml1$variants,
         cluster.col.name = 'cluster',
         show.cluster.size = FALSE,
         cluster.size.text.color = 'blue',
         vaf.col.names = aml1$params$vaf.col.names,
         sample.title.size = 20,
         violin = FALSE,
         box = FALSE,
         jitter = TRUE,
         jitter.color=c('#999793', '#8d4891', '#f8e356',
                     '#fe9536', '#d7352e'),
         display.plot=FALSE)