@@ -1,7 +1,7 @@

 Package: cellscape

 Title: Explores single cell copy number profiles in the context of a

 single cell tree

-Version: 1.27.0

+Version: 1.28.0

 Authors@R: c(

 person("Shixiang", "Wang", , "w_shixiang@163.com", role = c("aut", "cre"),

 comment = c(ORCID = "0000-0001-9855-7357")),

@@ -27,7 +27,6 @@ Imports:

 gtools (>= 3.5.0),

 htmlwidgets (>= 0.5),

 jsonlite (>= 0.9.19),

- plyr (>= 1.8.3),

 reshape2 (>=

 1.4.1),

 stringr (>= 1.0.0)

@@ -39,4 +38,4 @@ VignetteBuilder:

 biocViews: Visualization

 Encoding: UTF-8

 LazyData: true

-RoxygenNote: 6.0.1

+RoxygenNote: 7.2.3

@@ -16,3 +16,11 @@ export(getMutationsData)

 export(renderCnvTree)

 export(replaceSpaces)

 import(htmlwidgets)

+importFrom(reshape2,melt)

+importFrom(stats,coef)

+importFrom(stats,dist)

+importFrom(stats,hclust)

+importFrom(stats,lm)

+importFrom(stats,na.omit)

+importFrom(stats,setNames)

+importFrom(utils,combn)

@@ -56,7 +56,9 @@

 #'

 #'

 #' @import htmlwidgets

-#'

+#' @importFrom stats coef dist hclust lm na.omit setNames

+#' @importFrom utils combn

+#' @importFrom reshape2 melt

 #' @param cnv_data \code{data.frame}

 #' (Required if not providing mut_data nor mut_data_matrix)

 #' Single cell copy number segments data. Note that every single cell id

@@ -916,7 +918,12 @@ cellscape <- function(cnv_data = NULL,

 #' @export

 #' @rdname helpers

 #' @examples

-#' dfs_tree(data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7")), "1", c())

+#' dfs_tree(

+#' data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' ), "1", c()

+#' )

 dfs_tree <- function(edges, cur_root, dfs_arr) {

 if (!is.null(cur_root)) {

 # add this root to the dfs list of nodes

@@ -1329,7 +1336,7 @@ processUserData <- function(clonal_prev,

 perturbations <- checkPerts(perturbations)

 # MUTATIONS DATA

- mut_data <- getMutationsData(mutations, tree_edges, clonal_prev)

+ mut_data <- getMutationsData(mutations, tree_edges, clonal_prev, show_warnings)

 mutation_info <- mut_data$mutation_info

 mutation_prevalences <- mut_data$mutation_prevalences

 if (is.data.frame(mutations)) {

@@ -1410,12 +1417,26 @@ checkMinDims <- function(mutations, height, width) {

 #' @param tree_edges -- tree_edges provided by user

 #' @examples

 #' checkRequiredInputs(

-#' data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1", "2", "3", "4", "5", "6", "7"), clonal_prev = c("0.1", "0.22", "0.08", "0.53", "0.009", "0.061", "1")),

-#' data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7"))

+#' data.frame(

+#' timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+#' clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+#' clonal_prev = c("0.1", "0.22", "0.08", "0.53", "0.009", "0.061", "1")

+#' ),

+#' data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' )

 #' )

 #' checkRequiredInputs(

-#' data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1", "2", "3", "4", "5", "6", "7"), clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")),

-#' data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7"))

+#' data.frame(

+#' timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+#' clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+#' clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+#' ),

+#' data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' )

 #' )

 #' @export

 #' @rdname helpers

@@ -1476,7 +1497,12 @@ checkClonalPrev <- function(clonal_prev) {

 #'

 #' @param tree_edges -- tree edges provided by user

 #' @examples

-#' checkTreeEdges(data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7")))

+#' checkTreeEdges(

+#' data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' )

+#' )

 #' @export

 #' @rdname helpers

 checkTreeEdges <- function(tree_edges) {

@@ -1540,7 +1566,12 @@ checkGtypePositioning <- function(genotype_position) {

 #'

 #' @param clone_colours -- clone_colours provided by user

 #' @examples

-#' checkCloneColours(data.frame(clone_id = c("1", "2", "3", "4"), colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")))

+#' checkCloneColours(

+#' data.frame(

+#' clone_id = c("1", "2", "3", "4"),

+#' colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")

+#' )

+#' )

 #' @export

 #' @rdname helpers

 checkCloneColours <- function(clone_colours) {

@@ -1589,13 +1620,23 @@ checkPerts <- function(perturbations) {

 #' @param clonal_prev -- clonal prevalence data from user

 #' @examples

 #' getMutationsData(

-#' data.frame(chrom = c("11"), coord = c(104043), VAF = c(0.1), clone_id = c(1), timepoint = c("Relapse")),

-#' data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7")),

-#' data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1", "2", "3", "4", "5", "6", "7"), clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1"))

+#' data.frame(

+#' chrom = c("11"), coord = c(104043), VAF = c(0.1),

+#' clone_id = c(1), timepoint = c("Relapse")

+#' ),

+#' data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' ),

+#' data.frame(

+#' timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+#' clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+#' clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+#' )

 #' )

 #' @export

 #' @rdname helpers

-getMutationsData <- function(mutations, tree_edges, clonal_prev) {

+getMutationsData <- function(mutations, tree_edges, clonal_prev, show_warnings = TRUE) {

 if (is.data.frame(mutations)) {

 # ensure column names are correct

 if (!("chrom" %in% colnames(mutations)) ||

@@ -1712,11 +1753,27 @@ getMutationsData <- function(mutations, tree_edges, clonal_prev) {

 #' @rdname helpers

 #' @examples

 #' replaceSpaces(

-#' mutations = data.frame(chrom = c("11"), coord = c(104043), VAF = c(0.1), clone_id = c(1), timepoint = c("Relapse")),

-#' tree_edges = data.frame(source = c("1", "1", "2", "2", "5", "6"), target = c("2", "5", "3", "4", "6", "7")),

-#' clonal_prev = data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1", "2", "3", "4", "5", "6", "7"), clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")),

-#' mutation_prevalences = list("X:6154028" = data.frame(timepoint = c("Diagnosis"), VAF = c(0.5557))), mutation_info = data.frame(clone_id = c(1)),

-#' clone_colours = data.frame(clone_id = c("1", "2", "3", "4"), colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4"))

+#' mutations = data.frame(

+#' chrom = c("11"), coord = c(104043),

+#' VAF = c(0.1), clone_id = c(1), timepoint = c("Relapse")

+#' ),

+#' tree_edges = data.frame(

+#' source = c("1", "1", "2", "2", "5", "6"),

+#' target = c("2", "5", "3", "4", "6", "7")

+#' ),

+#' clonal_prev = data.frame(

+#' timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+#' clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+#' clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+#' ),

+#' mutation_prevalences = list(

+#' "X:6154028" = data.frame(timepoint = c("Diagnosis"), VAF = c(0.5557))

+#' ),

+#' mutation_info = data.frame(clone_id = c(1)),

+#' clone_colours = data.frame(

+#' clone_id = c("1", "2", "3", "4"),

+#' colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")

+#' )

 #' )

 replaceSpaces <- function(clonal_prev, tree_edges, clone_colours, mutation_info, mutations, mutation_prevalences) {

 # create map of original sample ids to space-replaced sample ids

new file mode 100644

@@ -0,0 +1,6 @@

+utils::globalVariables(

+ c("VAF", "chr", "chrom_index", "coord", "copy_number",

+ "cumsum_values", "genotype", "mode_cnv", "n",

+ "n_gt", "px", "px_width", "sc_id", "single_cell_id", "site",

+ "timepoint")

+)

\ No newline at end of file

@@ -4,18 +4,33 @@

 \alias{cellscape}

 \title{CellScape}

 \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)

+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{

-\item{cnv_data}{\code{data.frame} 

- (Required if not providing mut_data nor mut_data_matrix) 

+\item{cnv_data}{\code{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:

 \describe{

@@ -32,9 +47,9 @@ cellscape(cnv_data = NULL, mut_data = NULL, mut_data_matrix = NULL,

 }}

-\item{mut_data}{\code{data.frame} 

- (Required if not providing cnv_data nor mut_data_matrix) 

- Single cell targeted mutation data frame. Note that every single cell id 

+\item{mut_data}{\code{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:

 \describe{

@@ -48,22 +63,22 @@ cellscape(cnv_data = NULL, mut_data = NULL, mut_data_matrix = NULL,

 }}

-\item{mut_data_matrix}{\code{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 

+\item{mut_data_matrix}{\code{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.}

-\item{mut_order}{\code{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 

+\item{mut_order}{\code{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.}

-\item{tree_edges}{\code{data.frame} Edges for the single cell phylogenetic 

+\item{tree_edges}{\code{data.frame} Edges for the single cell phylogenetic

 tree. Required columns are:

 \describe{

@@ -79,7 +94,7 @@ determine mutation order.}

 }}

-\item{gtype_tree_edges}{\code{data.frame} (Required for TimeScape) Genotype 

+\item{gtype_tree_edges}{\code{data.frame} (Required for TimeScape) Genotype

 tree edges of a rooted tree. Required columns are:

 \describe{

@@ -89,7 +104,7 @@ determine mutation order.}

 }}

-\item{sc_annot}{\code{data.frame} (Required for TimeScape) Annotations 

+\item{sc_annot}{\code{data.frame} (Required for TimeScape) Annotations

 (genotype and sample id) for each single cell. Required columns are:

 \describe{

@@ -101,57 +116,57 @@ determine mutation order.}

 Optional columns are:

 \describe{

- \item{timepoint:}{\code{character()} id of the sampled time point. 

+ \item{timepoint:}{\code{character()} id of the sampled time point.

 Note: time points will be ordered alphabetically. }

 }}

-\item{clone_colours}{\code{data.frame} (Optional) Clone ids and their 

+\item{clone_colours}{\code{data.frame} (Optional) Clone ids and their

 corresponding colours (in hex format). Required columns are:

 \describe{

 \item{clone_id:}{\code{character()} clone id.}

- \item{colour:}{\code{character()} the corresponding Hex colour 

+ \item{colour:}{\code{character()} the corresponding Hex colour

 for each clone id.}

 }}

-\item{timepoint_title}{\code{character()} (Optional) Legend title for 

+\item{timepoint_title}{\code{character()} (Optional) Legend title for

 timepoint groups. Default is "Timepoint".}

-\item{clone_title}{\code{character()} (Optional) Legend title for clones. 

+\item{clone_title}{\code{character()} (Optional) Legend title for clones.

 Default is "Clone".}

-\item{xaxis_title}{\code{character()} (Optional) For TimeScape - x-axis title. 

+\item{xaxis_title}{\code{character()} (Optional) For TimeScape - x-axis title.

 Default is "Time Point".}

-\item{yaxis_title}{\code{character()} (Optional) For TimeScape - y-axis title. 

+\item{yaxis_title}{\code{character()} (Optional) For TimeScape - y-axis title.

 Default is "Clonal Prevalence".}

-\item{phylogeny_title}{\code{character()} (Optional) For TimeScape - legend 

+\item{phylogeny_title}{\code{character()} (Optional) For TimeScape - legend

 phylogeny title. Default is "Clonal Phylogeny".}

-\item{value_type}{\code{character()} (Optional) The type of value plotted in 

-heatmap - will affect legend and heatmap tooltips. Default is "VAF" for 

+\item{value_type}{\code{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.}

-\item{node_type}{\code{character()} (Optional) The type of node plotted in 

+\item{node_type}{\code{character()} (Optional) The type of node plotted in

 single cell phylogeny - will affect phylogeny tooltips. Default is "Cell".}

-\item{display_node_ids}{\code{logical()} (Optional) Whether or not to display 

+\item{display_node_ids}{\code{logical()} (Optional) Whether or not to display

 the single cell ID within the tree nodes. Default is FALSE.}

-\item{prop_of_clone_threshold}{\code{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. 

+\item{prop_of_clone_threshold}{\code{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.}

-\item{vaf_threshold}{\code{numeric()} (Optional) Used for the ordering of 

-targeted mutations. The minimum variant allele frequency for a mutation to 

+\item{vaf_threshold}{\code{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.}

-\item{show_warnings}{\code{logical()} (Optional) Whether or not to show any 

+\item{show_warnings}{\code{logical()} (Optional) Whether or not to show any

 warnings. Default is TRUE.}

 \item{width}{\code{numeric()} (Optional) Width of the plot.}

@@ -159,59 +174,59 @@ warnings. Default is TRUE.}

 \item{height}{\code{numeric()} (Optional) Height of the plot.}

 }

 \description{

-\code{cellscape} explores single cell copy number profiles in the 

+\code{cellscape} explores single cell copy number profiles in the

 context of a single cell phylogeny.

 }

 \details{

 Interactive components:

 \enumerate{

-\item Mouseover any single cell in the phylogeny to view its 

+ \item Mouseover any single cell in the phylogeny to view its

 corresponding genomic profile in the heatmap, and vice versa.

-\item Mouseover any part of the heatmap to view the CNV or VAF 

+ \item Mouseover any part of the heatmap to view the CNV or VAF

 value for that copy number segment or mutation site, respectively.

-\item Mouseover any branch of the phylogeny to view downstream 

+ \item Mouseover any branch of the phylogeny to view downstream

 single cells, both in the phylogeny and heatmap.

-\item Mouseover any clone to view its corresponding single cells 

+ \item Mouseover any clone to view its corresponding single cells

 in the phylogeny and heatmap.

-\item Click any node in the phylogeny to flip the order of its 

+ \item Click any node in the phylogeny to flip the order of its

 descendant branches.

-\item Use the selection tool in the tool bar to select single cell 

- genomic profiles and view their corresponding single cells in the 

+ \item Use the selection tool in the tool bar to select single cell

+ genomic profiles and view their corresponding single cells in the

 phylogeny.

-\item Use the tree trimming tool in the tool bar to remove any

+ \item Use the tree trimming tool in the tool bar to remove any

 branch of the phylogeny by clicking it.

-\item Use the switch view tool in the tool bar to change the 

- phylogeny view from force-directed to unidirectional, and vice 

+ \item Use the switch view tool in the tool bar to change the

+ phylogeny view from force-directed to unidirectional, and vice

 versa.

-\item Use the re-root phylogeny tool to root the phylogeny at a 

+ \item Use the re-root phylogeny tool to root the phylogeny at a

 clicked node.

-\item Use the flip branch tool to vertically rotate any branch by 

+ \item Use the flip branch tool to vertically rotate any branch by

 clicking its root node.

-\item If present, use the scale tree/graph tool in the tool bar to 

+ \item If present, use the scale tree/graph tool in the tool bar to

 scale the phylogeny by the provided edge distances.

-\item If time-series information is present such that the TimeScape 

- is displayed below the CellScape, clones and time points are 

+ \item 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.

-\item Click the download buttons to download a PNG or SVG of the view.

+ \item 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 

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

 information about TimeScape.

 }

 \examples{

@@ -223,50 +238,67 @@ library("cellscape")

 # EXAMPLE 1 - TARGETED MUTATION DATA

 # single cell tree edges

-tree_edges <- read.csv(system.file("extdata", "targeted_tree_edges.csv", 

- package = "cellscape"))

+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"))

+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"))

+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"))

+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())

+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)

+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"))

+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"))

+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")

+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"))

+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(

+ cnv_data = cnv_data, tree_edges = tree_edges, sc_annot = sc_annot,

+ width = 800, height = 475, show_warnings = FALSE,

+ clone_colours = clone_colours

+)

 }

@@ -50,9 +50,22 @@ getTargetedHeatmapForEachSC(mut_data, mut_order, heatmapWidth)

 findMode(x)

-processUserData(clonal_prev, tree_edges, mutations, clone_colours, xaxis_title,

- yaxis_title, phylogeny_title, alpha, genotype_position, perturbations, sort,

- show_warnings, width, height)

+processUserData(

+ clonal_prev,

+ tree_edges,

+ mutations,

+ clone_colours,

+ xaxis_title,

+ yaxis_title,

+ phylogeny_title,

+ alpha,

+ genotype_position,

+ perturbations,

+ sort,

+ show_warnings,

+ width,

+ height

+)

 checkMinDims(mutations, height, width)

@@ -70,10 +83,16 @@ checkCloneColours(clone_colours)

 checkPerts(perturbations)

-getMutationsData(mutations, tree_edges, clonal_prev)

+getMutationsData(mutations, tree_edges, clonal_prev, show_warnings = TRUE)

-replaceSpaces(clonal_prev, tree_edges, clone_colours, mutation_info, mutations,

- mutation_prevalences)

+replaceSpaces(

+ clonal_prev,

+ tree_edges,

+ clone_colours,

+ mutation_info,

+ mutations,

+ mutation_prevalences

+)

 }

 \arguments{

 \item{edges}{-- edges of tree}

@@ -84,9 +103,9 @@ replaceSpaces(clonal_prev, tree_edges, clone_colours, mutation_info, mutations,

 \item{outputId}{-- id of output}

-\item{width}{-- width of output}

+\item{width}{-- width provided by user}

-\item{height}{-- height of output}

+\item{height}{-- height provided by user}

 \item{expr}{-- expression for Shiny}

@@ -96,11 +115,11 @@ replaceSpaces(clonal_prev, tree_edges, clone_colours, mutation_info, mutations,

 \item{hm_sc_ids_ordered}{-- array of single cell ids in order}

-\item{ncols}{-- number of columns in heatmap/grid}

+\item{ncols}{-- integer of number of columns (pixels) to fill}

 \item{chroms}{-- vector of chromosome names}

-\item{cnv_data}{-- copy number data}

+\item{cnv_data}{-- data frame of copy number variant segments data}

 \item{chrom_bounds}{-- data frame of chromosome boundaries}

@@ -116,25 +135,13 @@ replaceSpaces(clonal_prev, tree_edges, clone_colours, mutation_info, mutations,

 \item{x}{-- vector of numbers}

-\item{clonal_prev}{-- data frame of Clonal prevalence. Note: timepoints will be alphanumerically sorted in the view.

-Format: columns are (1) character() "timepoint" - time point

- (2) character() "clone_id" - clone id

- (3) numeric() "clonal_prev" - clonal prevalence.}

+\item{clonal_prev}{-- clonal_prev data from user}

-\item{tree_edges}{-- data frame of Tree edges of a rooted tree.

-Format: columns are (1) character() "source" - source node id

- (2) character() "target" - target node id.}

+\item{tree_edges}{-- tree edges data from user}

-\item{mutations}{-- data frame (Optional) of Mutations occurring at each clone. Any additional field will be shown in the mutation table.

-Format: columns are (1) character() "chrom" - chromosome number

- (2) numeric() "coord" - coordinate of mutation on chromosome

- (3) character() "clone_id" - clone id

- (4) character() "timepoint" - time point

- (5) numeric() "VAF" - variant allele frequency of the mutation in the corresponding timepoint.}

+\item{mutations}{-- mutations data from user}

-\item{clone_colours}{-- data frame (Optional) of Clone ids and their corresponding colours 

-Format: columns are (1) character() "clone_id" - the clone ids

- (2) character() "colour" - the corresponding Hex colour for each clone id.}

+\item{clone_colours}{-- clone_colours data from user}

 \item{xaxis_title}{-- String (Optional) of x-axis title. Default is "Time Point".}

@@ -142,20 +149,14 @@ Format: columns are (1) character() "clone_id" - the clone ids

 \item{phylogeny_title}{-- String (Optional) of Legend phylogeny title. Default is "Clonal Phylogeny".}

-\item{alpha}{-- Number (Optional) of Alpha value for sweeps, range [0, 100].}

+\item{alpha}{-- alpha provided by user}

-\item{genotype_position}{-- String (Optional) of How to position the genotypes from ["centre", "stack", "space"] 

-"centre" -- genotypes are centred with respect to their ancestors

-"stack" -- genotypes are stacked such that no genotype is split at any time point

-"space" -- genotypes are stacked but with a bit of spacing at the bottom}

+\item{genotype_position}{-- genotype_position provided by user}

-\item{perturbations}{-- data frame (Optional) of any perturbations that occurred between two time points.

-Format: columns are (1) character() "pert_name" - the perturbation name

- (2) character() "prev_tp" - the time point (as labelled in clonal prevalence data) 

- BEFORE perturbation.}

+\item{perturbations}{-- perturbations provided by user}

-\item{sort}{-- Boolean (Optional) of whether (TRUE) or not (FALSE) to vertically sort the genotypes by their emergence values (descending). 

-Default is FALSE. 

+\item{sort}{-- Boolean (Optional) of whether (TRUE) or not (FALSE) to vertically sort the genotypes by their emergence values (descending).

+Default is FALSE.

 Note that genotype sorting will always retain the phylogenetic hierarchy, and this parameter will only affect the ordering of siblings.}

 \item{show_warnings}{-- Boolean (Optional) of Whether or not to show any warnings. Default is TRUE.}

@@ -163,60 +164,6 @@ Note that genotype sorting will always retain the phylogenetic hierarchy, and th

 \item{mutation_info}{-- processed mutation_info}

 \item{mutation_prevalences}{-- mutation_prevalences data from user}

-

-\item{chrom_bounds}{-- data frame of chromosome boundaries}

-

-\item{ncols}{-- integer of number of columns (pixels) to fill}

-

-\item{chrom_bounds}{-- data frame of chromosome boundaries}

-

-\item{cnv_data}{-- data frame of copy number variant segments data}

-

-\item{chrom_bounds}{-- data frame of chromosome boundaries}

-

-\item{n_bp_per_pixel}{-- integer of number of base pairs per pixel}

-

-\item{mut_data}{-- data frame of mutations data}

-

-\item{width}{-- Number (Optional) of width of the plot. Minimum width is 450.}

-

-\item{height}{-- Number (Optional) of height of the plot. Minimum height with and without mutations is 500 and 260, respectively.}

-

-\item{mutations}{-- mutations provided by user}

-

-\item{height}{-- height provided by user}

-

-\item{width}{-- width provided by user}

-

-\item{clonal_prev}{-- clonal_prev provided by user}

-

-\item{tree_edges}{-- tree_edges provided by user}

-

-\item{alpha}{-- alpha provided by user}

-

-\item{clonal_prev}{-- clonal prevalence provided by user}

-

-\item{tree_edges}{-- tree edges provided by user}

-

-\item{genotype_position}{-- genotype_position provided by user}

-

-\item{clone_colours}{-- clone_colours provided by user}

-

-\item{perturbations}{-- perturbations provided by user}

-

-\item{mutations}{-- mutations data from user}

-

-\item{tree_edges}{-- tree edges data from user}

-

-\item{clonal_prev}{-- clonal prevalence data from user}

-

-\item{clonal_prev}{-- clonal_prev data from user}

-

-\item{tree_edges}{-- tree edges data from user}

-

-\item{clone_colours}{-- clone_colours data from user}

-

-\item{mutations}{-- mutations data from user}

 }

 \description{

 Get depth first search of a tree

@@ -266,28 +213,91 @@ get mutation data

 function to replace spaces with underscores in all data frames & keep maps of original names to space-replaced names

 }

 \examples{

-dfs_tree(data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")), "1", c())

-cellscapeOutput(1, '100\%', '300px')

-cellscapeOutput(1, '80\%', '300px')

-findMode(c(1,1,19,1))

+dfs_tree(

+ data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ ), "1", c()

+)

+cellscapeOutput(1, "100\%", "300px")

+cellscapeOutput(1, "80\%", "300px")

+findMode(c(1, 1, 19, 1))

 checkMinDims(data.frame(chr = c("11"), coord = c(104043), VAF = c(0.1)), "700px", "700px")

-checkRequiredInputs(data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1","2","3","4","5","6","7"), clonal_prev = c("0.1","0.22","0.08","0.53","0.009","0.061","1")), 

-data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")))

-checkRequiredInputs(data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1","2","3","4","5","6","7"), clonal_prev = c("0.12","0.12","0.18","0.13","0.009","0.061","1")), 

-data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")))

+checkRequiredInputs(

+ data.frame(

+ timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+ clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+ clonal_prev = c("0.1", "0.22", "0.08", "0.53", "0.009", "0.061", "1")

+ ),

+ data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ )

+)

+checkRequiredInputs(

+ data.frame(

+ timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+ clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+ clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+ ),

+ data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ )

+)

 checkAlpha(4)

 checkAlpha(100)

-checkClonalPrev(data.frame(timepoint=c(1), clone_id=c(2), clonal_prev=c(0.1)))

-checkTreeEdges(data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")))

+checkClonalPrev(data.frame(timepoint = c(1), clone_id = c(2), clonal_prev = c(0.1)))

+checkTreeEdges(

+ data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ )

+)

 checkGtypePositioning("centre")

-checkCloneColours(data.frame(clone_id = c("1","2","3", "4"), colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")))

+checkCloneColours(

+ data.frame(

+ clone_id = c("1", "2", "3", "4"),

+ colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")

+ )

+)

 checkPerts(data.frame(pert_name = c("New Drug"), prev_tp = c("Diagnosis")))

-getMutationsData(data.frame(chrom = c("11"), coord = c(104043), VAF = c(0.1), clone_id=c(1), timepoint=c("Relapse")), 

-data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")), 

-data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1","2","3","4","5","6","7"), clonal_prev = c("0.12","0.12","0.18","0.13","0.009","0.061","1")))

-replaceSpaces(mutations = data.frame(chrom = c("11"), coord = c(104043), VAF = c(0.1), clone_id=c(1), timepoint=c("Relapse")), 

-tree_edges = data.frame(source = c("1","1","2","2","5","6"), target=c("2","5","3","4","6","7")), 

-clonal_prev = data.frame(timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)), clone_id = c("1","2","3","4","5","6","7"), clonal_prev = c("0.12","0.12","0.18","0.13","0.009","0.061","1")),

-mutation_prevalences = list("X:6154028" = data.frame(timepoint = c("Diagnosis"), VAF = c(0.5557))), mutation_info=data.frame(clone_id=c(1)),

-clone_colours = data.frame(clone_id = c("1","2","3", "4"), colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")))

+getMutationsData(

+ data.frame(

+ chrom = c("11"), coord = c(104043), VAF = c(0.1),

+ clone_id = c(1), timepoint = c("Relapse")

+ ),

+ data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ ),

+ data.frame(

+ timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+ clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+ clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+ )

+)

+replaceSpaces(

+ mutations = data.frame(

+ chrom = c("11"), coord = c(104043),

+ VAF = c(0.1), clone_id = c(1), timepoint = c("Relapse")

+ ),

+ tree_edges = data.frame(

+ source = c("1", "1", "2", "2", "5", "6"),

+ target = c("2", "5", "3", "4", "6", "7")

+ ),

+ clonal_prev = data.frame(

+ timepoint = c(rep("Diagnosis", 6), rep("Relapse", 1)),

+ clone_id = c("1", "2", "3", "4", "5", "6", "7"),

+ clonal_prev = c("0.12", "0.12", "0.18", "0.13", "0.009", "0.061", "1")

+ ),

+ mutation_prevalences = list(

+ "X:6154028" = data.frame(timepoint = c("Diagnosis"), VAF = c(0.5557))

+ ),

+ mutation_info = data.frame(clone_id = c(1)),

+ clone_colours = data.frame(

+ clone_id = c("1", "2", "3", "4"),

+ colour = c("#beaed4", "#fdc086", "#beaed4", "#beaed4")

+ )

+)

 }