longitudinal.tree.plot: longitudinal.tree.plot

In gian-asco/test: Longitudinal Analysis of Cancer Evolution (LACE)

longitudinal.tree.plot

Description

Plot a longitudinal tree inferred by LACE.

Usage

longitudinal.tree.plot(
  inference,
  rem_unseen_leafs = TRUE,
  show_plot = TRUE,
  filename = "lg_output.xml",
  labels_show = "mutations",
  clone_labels = NULL,
  show_prev = TRUE,
  label.cex = 1,
  size = 500,
  size2 = NULL,
  tk_plot = FALSE,
  tp_lines = TRUE,
  tp_mark = TRUE,
  tp_mark_alpha = 0.5,
  legend = TRUE,
  legend_position = "topright",
  label_offset = 4,
  legend_cex = 0.8
)

Arguments

inference	Results of the inference by LACE.
rem_unseen_leafs	If TRUE (default) remove all the leafs that have never been observed (prevalence = 0 in each time point)
show_plot	If TRUE (default) output the longitudinal tree to the current graphical device.
filename	Specify the name of the file where to save the longitudinal tree. Dot or graphml formats are supported and are chosen based on the extenction of the filename (.dot or .xml).
labels_show	Specify which type of label should be placed on the tree; options are, "mutations": parental edges are labeled with the acquired mutation between the two nodes (genotypes); "clones": nodes (genotypes) are labeled with their last acquired mutation; "both": either nodes and edges are labeled as specified above; "none": no labels will show on the longitudinal tree.
clone_labels	Character vector that specifies the name of the nodes (genotypes). If it is NULL (default), nodes will be labeled as specified by "label" parameter.
show_prev	If TRUE (default) add to clones label the correspongind prevalance.
label.cex	Specify the size of the labels.
size	Specify size of the nodes. The final area is proportional with the node prevalence.
size2	Specify the size of the second dimension of the nodes. If NULL (default), it is set equal to "size".
tk_plot	If TRUE, uses tkplot function from igraph library to plot an interactive tree. Default is FALSE.
tp_lines	If TRUE (defaul) the function draws lines between timepoints.
tp_mark	If TRUE (defaul) the function draws different colored area under the nodes in different time points.
tp_mark_alpha	Specify the alpha value of the area drawed when tp_mark = TRUE.
legend	If TRUE (default) a legend will be displayed on the plot.
legend_position	Specify the legend position.
label_offset	Move the mutation labels horizontally (default = 4)
legend_cex	Specify size of the legend text.

Value

An igraph object g with the longitudinal tree inferred by LACE.

Examples

data(inference)
clone_labels = c("ARPC2","PRAME","HNRNPC","COL1A2","RPL5","CCT8")
longitudinal.tree.plot(inference = inference,
                       labels = "clones",
                       clone_labels = clone_labels,
                       legend_position = "topleft")

gian-asco/test documentation built on April 11, 2022, 12:05 a.m.