Package 'CancerEvolutionVisualization'

Colour scheme vector

Description

Default colours used by CP polygons, etc.

Format

Character vector

---

CCF Distribution Heatmap

Description

Creates a heatmap of cancer cell fraction (CCF) distribution across tumour samples. The function is a wrapper around BoutrosLab.plotting.general::create.heatmap() with some changes in the default parameters. All parameter description are the same as in BoutrosLab.plotting.general::create.heatmap() except for ccf.thres.

Usage

create.ccf.heatmap(
    x,
    cluster.dimensions = 'both',
    clustering.method = 'complete',
    distance.method = 'euclidean',
    xaxis.lab = '',
    xlab.label = 'SNVs',
    print.colour.key = FALSE,
    colour.scheme = c('white', 'blue'),
    ...
    )

Arguments

x	Either a data-frame or a matrix from which the heatmap is to created
cluster.dimensions	Defaults to “both”.
clustering.method	Defaults to “complete”.
distance.method	Defaults to “euclidean”.
xaxis.lab	Defaults to an empty string.
xlab.label	Defaults to “SNVs”.
print.colour.key	Defaults to FALSE.
colour.scheme	Defaults to c('white', 'blue').
...	Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.

Value

A 'grob' object of the heatmap.

Author(s)

Helena Winata

See Also

create.heatmap

---

CCF Summary Heatmap

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 BoutrosLab.plotting.general::create.barplot() or BoutrosLab.plotting.general::create.heatmap() for parameter description. Legend parameters are passed to BoutrosLab.plotting.general::legend.grob().

Usage

create.ccf.summary.heatmap(
    DF,
    ccf.limits = NULL,
    median.col = 'median.ccf.per.sample',
    clone.order = NULL,
    sample.order = NULL,
    hm.col.scheme = c('white', 'blue'),
    clone.colours = NULL,
    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,
    legend.x = 0.9,
    legend.y = 0.8,
    plot.objects.heights = c(0.3, 1),
    add.median.text = FALSE,
    ...
    );

Arguments

DF	A data-frame with the following column names: 'ID', 'SNV.id', 'clone.id', 'CCF'.
ccf.limits	CCF limits to be applied to the heatmap. Must be a vector of length 2 for min and max thresholds. Defaults to NULL
median.col	Defaults to “median.ccf.per.sample”
clone.order	Defaults to NULL
sample.order	Defaults to NULL
hm.col.scheme	Heatmap colour scheme. Defaults to c('white', 'blue')
clone.colours	A named vector specifying the color to use for each clone to generate a covariate heatmap. If NULL, no covariates will be added.
subplot.xlab.cex	Subplot parameter. Defaults to 1.2
subplot.xaxis.cex	Subplot parameter. Defaults to 1
subplot.xaxis.fontface	Subplot parameter. Defaults to “bold”
subplot.xaxis.rot	Subplot parameter. Defaults to 90
subplot.ylab.cex	Subplot parameter. Defaults to 1.2
subplot.yaxis.cex	Subplot parameter. Defaults to 1
subplot.yaxis.fontface	Subplot parameter. Defaults to “bold”
hm.xaxis.rot	Subplot parameter. Defaults to 90
legend.size	Legend parameter. Defaults to 3
legend.title.cex	Legend parameter. Defaults to 1.2
legend.label.cex	Legend parameter. Defaults to 1
legend.x	Legend parameter. Defaults to 0.9
legend.y	Legend parameter. Defaults to 0.8
plot.objects.heights	If clone.colours is specified, this must be an array of length 3. Defaults to c(0.3, 1). See BoutrosLab.plotting.general::create.multipanelplot()
add.median.text	If TRUE, median CCF values will be added to the heatmap. Defaults to FALSE
...	Pass through argument. See BoutrosLab.plotting.general::create.multipanelplot() for further details.

Value

A 'grob' object of the summary plot.

Author(s)

Helena Winata

See Also

legend.grob, create.multipanelplot, create.heatmap

---

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,
    alpha = 0.25,
    legend.x = 0.1,
    legend.y = 0.55,
    ...
    )

Arguments

snv.df	A data frame containing the SNV data. It must have columns 'chr', 'pos', and 'clone.id'. If multi.sample = TRUE, it must also have a column 'ID' specifying the sample ID for each SNV.
genome.build	The genome build to use. Defaults to “GRCh37”.
clone.order	The order in which to plot the clones. If NULL, clones will be sorted alphabetically.
clone.colours	A named vector specifying the color to use for each clone. If NULL, colors will be automatically assigned.
filename	Directory or filepath to save the plot in. If multi.sample = TRUE, this must be a directory. if multi.sample = FALSE, this must be a filepath. If NULL, the plot will not be saved.
multi.sample	Logical indicating whether the input data contains multiple samples. Defaults to FALSE.
alpha	Transparency level of the points in the scatter plot. Defaults to 0.25.
legend.x	Legend parameter. Defaults to 0.1
legend.y	Legend parameter. Defaults to 0.55
...	Additional arguments to be passed to 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(s)

Helena Winata, Selina Wu

See Also

legend.grob, create.multipanelplot, create.scatterplot, create.densityplot

---

Cluster Heatmap

Description

Creates a heatmap of cancer cell fraction (CCF) distribution across tumour samples with clone IDs as a covariate beneath the heatmap.

Usage

create.cluster.heatmap(
    DF,
    ccf.limits = NULL,
    clone.colours = NULL,
    height = 6,
    width = 11,
    xaxis.col = NULL,
    legend.size = 3,
    legend.title.cex = 1.2,
    legend.label.cex = 1,
    filename = NULL,
    xlab.label = 'SNVs',
    xlab.cex = 1.2,
    xaxis.cex = 1,
    xaxis.fontface = 'bold',
    y.spacing = 1,
    colour.scheme = c('white', 'blue'),
    ...
    );

Arguments

DF	A data-frame with the following column names: 'ID', 'SNV.id', 'clone.id', 'CCF'.
ccf.limits	CCF limits to be applied to the heatmap. Must be a vector of length 2 for min and max thresholds. Defaults to NULL
clone.colours	Named list to provide a colour scheme for the clone ID covariate bar. If NULL, colours will be randomly generated. Defaults to NULL.
height	Defaults to 6
width	Defaults to 11
xaxis.col	Column in DF to extract x-axis labels from. Defaults to NULL.
legend.size	Width of the legend boxes in 'character' units. Defaults to 3
legend.title.cex	Size of titles in the legends. Defaults to 1.2
legend.label.cex	Size of text labels in the legends. Defaults to 1
filename	Filename for tiff output, or if NULL returns the trellis object itself. Defaults to NULL.
xlab.label	Defaults to “SNVs”.
xlab.cex	Defaults to 1.2
xaxis.cex	Defaults to 1
xaxis.fontface	Defaults to “bold”.
y.spacing	Spacing between heatmap and clone covariate bar. Defaults to 1
colour.scheme	Colour scheme for the heatmap. Defaults to c('white', 'blue').
...	Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.

Value

A 'grob' object of the heatmap.

Author(s)

Helena Winata

See Also

create.ccf.heatmap, create.heatmap

---

Phylogenetic Tree Plot

Description

Create a phylogenetic tree plot using 'SRCGrob'. The 'width', 'heigth', 'units', 'res', and 'bg' arguments are passed to the 'grDevices' function to save the plot to file.

Usage

create.phylogenetic.tree(
    tree,
    filename = NULL,
    width = 5,
    height = 5,
    units = 'in',
    res = 500,
    bg = 'white',
    ...
    )

Arguments

tree	Tree structure data.frame
filename	Filename for plot output, or if NULL displays the tree using grid.draw. Defaults to NULL.
width	Width of the plot. Defaults to 5.
height	Height of the plot. Defaults to 5.
units	Units of the plot. Defaults to “in”.
res	Resolution of the plot. Defaults to 500.
bg	Background colour of the plot. Defaults to “white”.
...	Pass through argument. See SRCGrob() for further details.

Value

A 'grob' of class "SRCGrob".

Author(s)

Helena Winata

See Also

SRCGrob, pdf, png, tiff, svg

Examples

# Simple Tree Plot
simple.tree <- data.frame(
    parent = c(NA, 1, 1)
    );
create.phylogenetic.tree(simple.tree);

# Non-numeric node.id
phy.dt <- data.frame(
    node.id = c('MRCA', 'C01', 'C02', 'C03', 5:7),
    parent = c(NA, 'MRCA', 'MRCA', 'MRCA', 'C02', 'C03', 'C03')
    );
create.phylogenetic.tree(phy.dt);

# Numeric disordered node.id with labels
phy.dt <- data.frame(
    node.id = c(1, 2, 5, 6, 4, 9, 10),
    parent = c(NA, 1, 1, 1, 5, 6, 6),
    label = c('MRCA', 'C01', 'C02', 'C03', 5:7)
    );
create.phylogenetic.tree(phy.dt);

---

GRCh37 Chromosom Information

Description

Chromosome information for the GRCh37 genome build. Used for plotting.

Format

data.frame

---

GRCh38 Chromosom Information

Description

Chromosome information for the GRCh38 genome build. Used for plotting.

Format

data.frame

---

Subclone Tree Plot

Description

Creates a phylogenetic tree using subclonal reconstruction data. An optional node text data.frame can be used to annotate notable genes alonside branches.

Usage

SRCGrob(
    tree,
    node.text = NULL,
    main = NULL,
    horizontal.padding = 0.1,
    scale1 = 1,
    scale2 = 1,
    yat = NULL,
    yaxis1.label = NULL,
    yaxis2.label = NULL,
    xlab.cex = 1.55,
    ylab.cex = 1.55,
    xaxis.cex = 1.45,
    yaxis.cex = 1.45,
    xaxis.label = 'CP',
    label.cex = NA,
    node.text.cex = 0.85,
    main.y = NULL,
    main.cex = 1.7,
    node.text.line.dist = 0.1,
    colour.scheme = 'grey',
    add.normal = FALSE,
    use.radians = FALSE,
    normal.cex = 1,
    label.nodes = TRUE,
    disable.polygons = FALSE,
    polygon.shape = 3,
    polygon.width = 1.2,
    length.from.node.edge = TRUE,
    size.units = 'npc',
    scale.bar = FALSE,
    scale.bar.coords = c(0.5, 1),
    scale.size.1 = NA,
    scale.size.2 = NA,
    scale.padding = 1

    );

Arguments

tree	Tree structure data.frame
node.text	Dataframe for text labels to be displayed next to nodes
main	Main plot title
horizontal.padding	Increase/reduce the plot's horizontal padding proportionally. A positive value will expand the padding, and a negative value will reduce it.
scale1	Proportionally scale the values of the first branch length column in the tree input.
scale2	Proportionally scale the values of the second branch length column in the tree input.
yat	Specific values to be used for the y-axis ticks. A list is required, with each element corresponding to an axis.
yaxis1.label	Text label for the first, leftmost y-axis
yaxis2.label	Text label for the second, rightmost y-axis
xlab.cex	Font size for the x-axis label
ylab.cex	Font size for the y-axis labels
xaxis.cex	Font size for the x-axis tick labels
yaxis.cex	Font size for the y-axis tick labels
xaxis.label	Text label for the x-axis
label.cex	Font size for the node labels
node.text.cex	Font size for the node text
main.y	Move the main plot title position up or down
main.cex	Font size for the main plot title
node.text.line.dist	Distance between node text and tree branches (as a value between 0 and 1)
colour.scheme	Vector of colour values to be used for CP polygons
add.normal	Adds a normal
use.radians	Unit to be used for 'angle' column (degrees or radians)
normal.cex	Font size within the normal 'box'
label.nodes	Enable/disable node labels
disable.polygons	Disables CP polygon drawing (even when CP values are provided)
polygon.shape	Changes the shape of the CP shading. Lower values are smoother.
polygon.width	Width of the CP shading
length.from.node.edge	Sets the branch length to be calculated from the edge of the node instead of the centre
size.units	Grid units to be used for all specific size/length parameters
scale.bar	Set to TRUE to add a scale bar instead of y-axis
scale.bar.coords	Coordinates for the scale bar placement c(x.pos, y.pos)
scale.size.1	Overide size of the first scale bar
scale.size.2	Overide size of the second scale bar
scale.padding	Padding between scale bars if more than 1 is present

Value

A ‘grob' of class ’SRCGrob'

Author(s)

Dan Knight

Examples

# Simple Tree Plot
simple.tree <- data.frame(
    parent = c(NA, 1, 1)
    );

SRCGrob(simple.tree);


# Specify Branch Lengths
branch.lengths.tree <- data.frame(
    simple.tree,
    length1 = c(10, 20, 15)
    );

SRCGrob(branch.lengths.tree);


# Cellular Prevalence
CP.tree <- data.frame(
    branch.lengths.tree,
    CP = c(1, 0.3, 0.5)
    );

SRCGrob(CP.tree);


# Scaled Branch Lengths
SRCGrob(
    branch.lengths.tree,
    scale1 = 0.8
    );


# Override Branch Angles in Degrees
degrees.tree <- data.frame(
    parent = c(NA, 1, 2),
    angle = c(NA, NA, 90)
    );

SRCGrob(degrees.tree);


# Override Branch Angles in Radians
radians.tree <- data.frame(
    parent = c(NA, 1, 2),
    angle = c(NA, NA, pi / 2)
    );

SRCGrob(
    radians.tree,
    use.radians = TRUE
    );


# Plot Title
SRCGrob(
    simple.tree,
    main = 'Example Plot'
    );


# Y-Axis Label
SRCGrob(
    branch.lengths.tree,
    yaxis1.label = 'SNVs'
    );


# Y-Axis Ticks
yaxis1.ticks <- seq(0, 10, 2);

SRCGrob(
    branch.lengths.tree,
    yat = list(yaxis1.ticks)
    );


# Scale Bar
SRCGrob(
    branch.lengths.tree,
    yaxis1.label = 'SNVs',
    scale.bar = TRUE
    );


# Normal
SRCGrob(
    simple.tree,
    add.normal = TRUE
    );


# Nodeless Mode
nodeless.tree <- data.frame(
    parent = c(NA, 1, 2, 2),
    draw.node = c(TRUE, FALSE, TRUE, TRUE)
    );

SRCGrob(nodeless.tree);

---