Add documentation and examples for new functions; enhance existing fu…

DESCRIPTION

@@ -4,13 +4,13 @@ Title: Single Cell Oriented Reconstruction of PANDA Individually Optimized Netwo
 Version: 1.3.3
 Authors@R: c(person("Daniel","Osorio", email = "daniecos@uio.no", role = c("aut","cre"), comment = c(ORCID = "0000-0003-4424-8422")),
   person("Marieke L.","Kuijjer", email = "marieke.kuijjer@ncmbm.uio.no", role = c("aut"), comment = c(ORCID = "0000-0001-6280-3130")))
-Description: Constructs cell-type–specific gene regulatory networks from single-cell RNA-sequencing data. The method implements the SCORPION algorithm, which first aggregates individual cells into super-cells and then applies PANDA (Passing Attributes between Networks for Data Assimilation) to infer transcription factor–target regulatory relationships. It also provides statistical methods for differential edge analysis.
+Description: Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data. The method implements the SCORPION algorithm, which first aggregates individual cells into super-cells and then applies PANDA (Passing Attributes between Networks for Data Assimilation) to infer transcription factor-target regulatory relationships. It also provides statistical methods for differential edge analysis.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.5.0)
 Imports: cli, methods, irlba, igraph, RANN, Matrix, pbapply, dplyr, furrr, future
-Suggests: RhpcBLASctl, testthat, mori
+Suggests: RhpcBLASctl, testthat, mori, circlize, biomaRt, fgsea
 URL: https://github.com/kuijjerlab/SCORPION
 BugReports: https://github.com/kuijjerlab/SCORPION/issues
 RoxygenNote: 7.3.3

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(circosEdges)
+export(enrichEdges)
+export(maEdges)
 export(regressEdges)
 export(runSCORPION)
 export(scorpion)
@@ -11,6 +14,7 @@ importFrom(RANN,nn2)
 importFrom(cli,cli_abort)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
+importFrom(cli,cli_alert_warning)
 importFrom(cli,cli_h1)
 importFrom(cli,cli_progress_along)
 importFrom(dplyr,"%>%")
@@ -23,6 +27,9 @@ importFrom(furrr,future_map)
 importFrom(future,multisession)
 importFrom(future,plan)
 importFrom(future,sequential)
+importFrom(grDevices,adjustcolor)
+importFrom(grDevices,hcl.colors)
+importFrom(graphics,legend)
 importFrom(igraph,cluster_louvain)
 importFrom(igraph,cluster_walktrap)
 importFrom(igraph,contract)

R/data-scorpionTest.R

@@ -1,37 +1,32 @@
 #' @name scorpionTest
 #' @docType data
-#' @title Example single-cell gene expression, motif, and ppi data
-#' @description This data is a list containing three objects. The motif \code{data.frame} describes a set of pairwise connections where a specific known sequence motif of a transcription factor was found upstream of the corresponding gene. The expression \code{dgCMatrix} is a set of 230 gene expression levels measured across 80 cells. Finally, the ppi \code{data.frame} describes a set of known pairwise protein-protein interactions.
+#' @title Example single-cell colorectal cancer data for SCORPION
+#' @description
+#' A list bundling the inputs required to build and compare gene regulatory
+#' networks with SCORPION, derived from a colorectal cancer single-cell
+#' RNA-sequencing experiment. It contains a gene expression matrix, a
+#' transcription factor motif prior, a protein-protein interaction prior, and
+#' cell-level metadata.
 #' @usage data(scorpionTest)
-#' @format A list containing three datasets.
+#' @format A named list with four elements:
 #' \describe{
-#' \item{\code{gex}}{A subsetted version of 10X Genomics' 3k PBMC dataset provided by the \code{Seurat} package.}
-#' \item{\code{tf}}{Subset of the transcription-factor and target gene list provided by the \code{dorothea} package for Homo sapiens.}
-#' \item{\code{ppi}}{The known protein-protein interactions and the combined score downloaded from the STRING database}
+#'   \item{\code{gex}}{A \code{dgCMatrix} gene expression matrix with 300 genes
+#'     (rows) and 1,954 cells (columns).}
+#'   \item{\code{tf}}{A \code{data.frame} of transcription factor-target motif
+#'     pairs from DoRothEA with columns \code{source_genesymbol},
+#'     \code{target_genesymbol} and \code{weight} (371,738 rows).}
+#'   \item{\code{ppi}}{A \code{data.frame} of protein-protein interactions with
+#'     columns \code{source_genesymbol}, \code{target_genesymbol} and
+#'     \code{weight} (4,076 rows).}
+#'   \item{\code{metadata}}{A \code{data.frame} of cell-level annotations with
+#'     columns \code{cell_id}, \code{donor}, \code{region} and \code{cell_type}
+#'     (1,954 rows). Region codes are \code{T} (tumor), \code{B} (border) and
+#'     \code{N} (normal).}
 #' }
 #' @examples
 #' # Loading example data
 #' data(scorpionTest)
 #'
 #' # The structure of the data
 #' str(scorpionTest)
-#'
-#' # List of 3
-#' # $ gex:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
-#' # .. ..@ i       : int [1:4456] 1 5 8 11 22 30 33 34 36 38 ...
-#' # .. ..@ p       : int [1:81] 0 47 99 149 205 258 306 342 387 423 ...
-#' # .. ..@ Dim     : int [1:2] 230 80
-#' # .. ..@ Dimnames:List of 2
-#' # .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
-#' # .. .. ..$ : chr [1:80] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
-#' # .. ..@ x       : num [1:4456] 1 1 3 1 1 4 1 5 1 1 ...
-#' # .. ..@ factors : list()
-#' # $ tf :'data.frame':	4485 obs. of  3 variables:
-#' #   ..$ tf    : chr [1:4485] "ADNP" "ADNP" "ADNP" "AEBP2" ...
-#' # ..$ target: chr [1:4485] "PRF1" "TMEM40" "TNFRSF1B" "CFP" ...
-#' # ..$ mor   : num [1:4485] 1 1 1 1 1 1 1 1 1 1 ...
-#' # $ ppi:'data.frame':	12754 obs. of  3 variables:
-#' #   ..$ X.node1       : chr [1:12754] "ADNP" "ADNP" "ADNP" "AEBP2" ...
-#' # ..$ node2         : chr [1:12754] "ZBTB14" "NFIA" "CDC5L" "YY1" ...
-#' # ..$ combined_score: num [1:12754] 0.769 0.64 0.581 0.597 0.54 0.753 0.659 0.548 0.59 0.654 ...
 NULL