cellscape: CellScape

In cellscape: Explores single cell copy number profiles in the context of a single cell tree

Description

cellscape explores single cell copy number profiles in the context of a single cell phylogeny.

Usage

cellscape(cnv_data = NULL, mut_data = NULL, mut_data_matrix = NULL,
  mut_order = NULL, tree_edges, gtype_tree_edges = NULL, sc_annot = NULL,
  clone_colours = "NA", timepoint_title = "Timepoint",
  clone_title = "Clone", xaxis_title = "Time Point",
  yaxis_title = "Clonal Prevalence", phylogeny_title = "Clonal Phylogeny",
  value_type = NULL, node_type = "Cell", display_node_ids = FALSE,
  prop_of_clone_threshold = 0.2, vaf_threshold = 0.05,
  show_warnings = TRUE, width = 900, height = 800)

Arguments

cnv_data	data.frame (Required if not providing mut_data nor mut_data_matrix) Single cell copy number segments data. Note that every single cell id must be present in the tree_edges data frame. Required columns are: single_cell_id: character() single cell id. chr: character() chromosome number. start: numeric() start position. end: numeric() end position. copy_number: numeric() copy number state.
mut_data	data.frame (Required if not providing cnv_data nor mut_data_matrix) Single cell targeted mutation data frame. Note that every single cell id must be present in the tree_edges data frame. Required columns are: single_cell_id: character() single cell id. chr: character() chromosome number. coord: numeric() genomic coordinate. VAF: numeric() variant allele frequency [0, 1].
mut_data_matrix	matrix (Required if not providing cnv_data nor mut_data) Single cell targeted mutation matrix. Rows are single cell IDs, columns are mutations. Rows and columns must be named, column names in the format "<chromosome>:<coordinate>". Note that the order of these rows and columns will not be preserved, unless mutation order is the same as that specified in the mut_order parameter. Also note that every single cell id must be present in the tree_edges data frame.
mut_order	vector (Optional) Mutation order for targeted mutation heatmap (each mutation should consist of a string in the form "chrom:coord"). Default will use a clustering function to determine mutation order.
tree_edges	data.frame Edges for the single cell phylogenetic tree. Required columns are: source: character() edge source (single cell id). target: character() edge target (single cell id). Optional columns are: dist: numeric() edge distance.
gtype_tree_edges	data.frame (Required for TimeScape) Genotype tree edges of a rooted tree. Required columns are: source: character() source node id. target: character() target node id.
sc_annot	data.frame (Required for TimeScape) Annotations (genotype and sample id) for each single cell. Required columns are: single_cell_id: character() single cell id. genotype: character() genotype assignment. Optional columns are: timepoint: character() id of the sampled time point. Note: time points will be ordered alphabetically.
clone_colours	data.frame (Optional) Clone ids and their corresponding colours (in hex format). Required columns are: clone_id: character() clone id. colour: character() the corresponding Hex colour for each clone id.
timepoint_title	character() (Optional) Legend title for timepoint groups. Default is "Timepoint".
clone_title	character() (Optional) Legend title for clones. Default is "Clone".
xaxis_title	character() (Optional) For TimeScape - x-axis title. Default is "Time Point".
yaxis_title	character() (Optional) For TimeScape - y-axis title. Default is "Clonal Prevalence".
phylogeny_title	character() (Optional) For TimeScape - legend phylogeny title. Default is "Clonal Phylogeny".
value_type	character() (Optional) The type of value plotted in heatmap - will affect legend and heatmap tooltips. Default is "VAF" for mutation data, and "CNV" for copy number data.
node_type	character() (Optional) The type of node plotted in single cell phylogeny - will affect phylogeny tooltips. Default is "Cell".
display_node_ids	logical() (Optional) Whether or not to display the single cell ID within the tree nodes. Default is FALSE.
prop_of_clone_threshold	numeric() (Optional) Used for the ordering of targeted mutations. The minimum proportion of a clone to have a mutation in order to consider the mutation as present within that clone. Default is 0.2.
vaf_threshold	numeric() (Optional) Used for the ordering of targeted mutations. The minimum variant allele frequency for a mutation to be considered as present within a single cell. Default is 0.05.
show_warnings	logical() (Optional) Whether or not to show any warnings. Default is TRUE.
width	numeric() (Optional) Width of the plot.
height	numeric() (Optional) Height of the plot.

Details

Interactive components:

1. Mouseover any single cell in the phylogeny to view its corresponding genomic profile in the heatmap, and vice versa.

2. Mouseover any part of the heatmap to view the CNV or VAF value for that copy number segment or mutation site, respectively.

3. Mouseover any branch of the phylogeny to view downstream single cells, both in the phylogeny and heatmap.

4. Mouseover any clone to view its corresponding single cells in the phylogeny and heatmap.

5. Click any node in the phylogeny to flip the order of its descendant branches.

6. Use the selection tool in the tool bar to select single cell genomic profiles and view their corresponding single cells in the phylogeny.

7. Use the tree trimming tool in the tool bar to remove any branch of the phylogeny by clicking it.

8. Use the switch view tool in the tool bar to change the phylogeny view from force-directed to unidirectional, and vice versa.

9. Use the re-root phylogeny tool to root the phylogeny at a clicked node.

10. Use the flip branch tool to vertically rotate any branch by clicking its root node.

11. If present, use the scale tree/graph tool in the tool bar to scale the phylogeny by the provided edge distances.

12. If time-series information is present such that the TimeScape is displayed below the CellScape, clones and time points are interactively linked in both views on mouseover.

13. Click the download buttons to download a PNG or SVG of the view.

Note:

See TimeScape repo (https://bitbucket.org/MO_BCCRC/timescape) for more information about TimeScape.

Examples

library("cellscape")


# EXAMPLE 1 - TARGETED MUTATION DATA

# single cell tree edges
tree_edges <- read.csv(system.file("extdata", "targeted_tree_edges.csv", 
    package = "cellscape"))

# targeted mutations
targeted_data <- read.csv(system.file("extdata", "targeted_muts.csv", 
    package = "cellscape"))

# genotype tree edges
gtype_tree_edges <- data.frame("source"=c("Ancestral", "Ancestral", "B",
    "C", "D"), "target"=c("A", "B", "C", "D", "E"))

# annotations
sc_annot <- read.csv(system.file("extdata", "targeted_annots.csv", 
    package = "cellscape"))

# mutation order
mut_order <- scan(system.file("extdata", "targeted_mut_order.txt", 
    package = "cellscape"), what=character())

# run cellscape
cellscape(mut_data=targeted_data, tree_edges=tree_edges, sc_annot = 
    sc_annot, gtype_tree_edges=gtype_tree_edges, mut_order=mut_order)


# EXAMPLE 2 - COPY NUMBER DATA

# single cell tree edges
tree_edges <- read.csv(system.file("extdata", "cnv_tree_edges.csv", 
    package = "cellscape"))

# cnv segments data
cnv_data <- read.csv(system.file("extdata", "cnv_data.csv", package = 
    "cellscape"))

# annotations
sc_annot <- read.csv(system.file("extdata", "cnv_annots.tsv", package = 
    "cellscape"), sep="\t")

# custom clone colours
clone_colours <- data.frame( clone_id = c("1","2","3"), 
    colour = c("7fc97f", "beaed4", "fdc086"))

# run cellscape
cellscape(cnv_data=cnv_data, tree_edges=tree_edges, sc_annot=sc_annot, 
    width=800, height=475, show_warnings=FALSE, 
    clone_colours = clone_colours)

cellscape documentation built on Nov. 8, 2020, 5:02 p.m.