Merge pull request #2 from spriyansh/multi_lineage

v0.04

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scMaSigPro
 Type: Package
 Title: Application of MaSigPro Bioconductor Package for scRNA Trajectory data
-Version: 0.0.3
+Version: 0.0.4
 Authors@R: c(
     person("Ana", "Conesa", role = c("aut"), email = "ana.conesa@csic.es"),
     person("Maria Jose", "Nueda", role = c("aut"), email = "mj.nueda@ua.es"),
@@ -14,10 +14,9 @@ Description: scMaSigPro is a polynomial regression-based approach inspired by
     significant expression profile differences among branching paths.
 License: GPL (>= 2)
 Imports:
-    assertthat, e1071, dplyr, entropy, ggplot2, igraph, magrittr, maSigPro,
-    MASS, MatrixGenerics, methods, parallel, parallelly, plotly, RColorConesa,
-    rlang, S4Vectors, scales, shiny, SingleCellExperiment, stats, stringr,
-    utils, mclust
+    assertthat, e1071, dplyr, entropy, ggplot2, igraph, magrittr, maSigPro (>= 1.74.0),
+    MASS, MatrixGenerics (>= 1.14.0), methods, parallel, parallelly, plotly, rlang, 
+    S4Vectors (>= 0.40.2), scales, shiny, SingleCellExperiment (>= 1.24.0), stats, stringr, utils, mclust
 Depends: R (>= 4.0)
 Encoding: UTF-8
 LazyData: true
@@ -28,7 +27,6 @@ Suggests:
     knitr,
     rmarkdown,
     BiocStyle,
-    ComplexUpset,
     UpSetR,
     ggpubr
 Config/testthat/edition: 3

NAMESPACE

@@ -15,6 +15,7 @@ export(eDense)
 export(eSparse)
 export(m3_select_path)
 export(pathAssign)
+export(pb_counts)
 export(plotBinTile)
 export(plotDiagnostics)
 export(plotIntersect)
@@ -25,6 +26,7 @@ export(queryCoeff)
 export(sc.cluster.trend)
 export(sc.filter)
 export(sc.p.vector)
+export(sc.restruct)
 export(sc.set.poly)
 export(sc.squeeze)
 export(sc.t.fit)
@@ -54,15 +56,12 @@ importFrom(MASS,glm.nb)
 importFrom(MASS,negative.binomial)
 importFrom(MatrixGenerics,rowMeans)
 importFrom(MatrixGenerics,rowSums)
-importFrom(RColorConesa,colorConesa)
-importFrom(RColorConesa,getConesaColors)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isEmpty)
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,colData)
 importFrom(SingleCellExperiment,reducedDims)
-importFrom(assertthat,assert_that)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
@@ -84,7 +83,6 @@ importFrom(entropy,discretize)
 importFrom(igraph,get.data.frame)
 importFrom(maSigPro,get.siggenes)
 importFrom(maSigPro,make.design.matrix)
-importFrom(maSigPro,position)
 importFrom(maSigPro,reg.coeffs)
 importFrom(magrittr,"%>%")
 importFrom(mclust,Mclust)
@@ -160,10 +158,6 @@ importFrom(stats,residuals)
 importFrom(stats,rstandard)
 importFrom(stats,sd)
 importFrom(stats,setNames)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_remove_all)
-importFrom(stringr,str_split)
-importFrom(stringr,str_split_i)
 importFrom(utils,View)
 importFrom(utils,combn)
 importFrom(utils,data)

NEWS.md

@@ -0,0 +1,50 @@
+## scMaSigPro 0.0.4 (2024-07-30)
+
+* Dependency Changes
+    * Removed hard dependency on `RColorConesa` and `ComplexUpset`.
+    * Removed `assertthat`, `stringr` from namespace.
+    * Removed `maSigPro::position` from namespace.
+
+* Plotting Updates
+    * Updated plot functions to use a custom palette.
+    * Updated `plotTrendCluster` function for distinct layers.
+    * Enhanced `plotIntersect()` with return capabilities.
+    * Enhanced `plotTrend` with curves, lines, and points.
+    * Updated ordering by frequency in `UpsetR`.
+
+* Function Updates
+    * Added `clean_string()` internal function.
+    * Added `sc.restruct()` function.
+    * Exported `pb_helpers()`.
+
+* Documentation Updates
+    * General code styling.
+    * Updated README with citation information.
+    * Single comprehensive data documentation.
+    * Added a new vignette.
+
+* Bug Fixes
+    * Removed `patchwork` call.
+
+## scMaSigPro 0.0.3 (2024-03-3)
+
+* Bug fixes
+    * `eSparse()` and `eDense()` indexes
+    * Removed the ComplexUpset error due to ggplot 3.5.0.
+
+* Remove Package Dependence
+    * SummarizedExperiment
+    * ComplexUpset
+
+* Package Suggestions Added
+    * Patchwork
+    * ComplexUpset
+    * UpSetR
+
+* Updated Test cases
+    * Functionality of `eSparse()` and `eDense()`
+    * Testing `sc.squeeze()` against manual pseudo-bulking
+
+## scMaSigPro 0.0.1 (2023-12-20)
+
+* Initial Github release.

R/annotate_sce.R

@@ -7,7 +7,6 @@
 #' \pkg{SingleCellExperiment} package.
 #'
 #' @importFrom SingleCellExperiment colData
-#' @importFrom assertthat assert_that
 #'
 #' @param sce A `SingleCellExperiment` object to be annotated.
 #' @param ptime_col A character string representing the column name
@@ -41,7 +40,7 @@ annotate_sce <- function(sce,
                          verbose = TRUE) {
   # Overwite the columns
   if (labels_exist) {
-    assert_that(
+    assertthat::assert_that(
       all(!is.null(exist_ptime_col) & !is.null(exist_path_col)),
       msg = paste(
         "Requested to set 'path_col' as", path_col,
@@ -62,12 +61,12 @@ annotate_sce <- function(sce,
     cell.meta <- as.data.frame(colData(sce))
 
     # Check columns
-    assert_that(
+    assertthat::assert_that(
       all(exist_ptime_col %in% colnames(cell.meta)),
       msg = paste("'", exist_ptime_col, "', doesn't exist in colData.")
     )
     # Check columns
-    assert_that(
+    assertthat::assert_that(
       all(exist_path_col %in% colnames(cell.meta)),
       msg = paste("'", exist_path_col, "', doesn't exist in colData")
     )

R/as_scmp.R

@@ -6,7 +6,6 @@
 #' SingleCellExperiment #' object to an instance of the scmpClass object.
 #'
 #' @importFrom SingleCellExperiment SingleCellExperiment
-#' @importFrom assertthat assert_that
 #'
 #' @param object An S4 object of class `cds/CellDataSet` or `SingleCellExperiment`.
 #' @param from Character string specifying the class of 'object'. Use "cds" for
@@ -65,32 +64,32 @@ as_scmp <- function(object, from = "cds",
                       labels_exist = FALSE
                     )) {
   # Check Conversion Type
-  assert_that(from %in% c("cds", "sce"),
+  assertthat::assert_that(from %in% c("cds", "sce"),
     msg = ("Currently, accepted options in the 'from' parameter are 'cds'
     ('cds/CellDataSet' object) and 'sce' ('SingleCellExperiment').")
   )
 
   # Validate S4
-  assert_that(
+  assertthat::assert_that(
     all(isS4(object) & all(is(object, "cell_data_set") | is(object, "SingleCellExperiment"))),
     msg = "Please provide object from one of the class 'cds/CellDataSet',
     or 'SingleCellExperiment/sce'."
   )
 
   # Check and validate additional parameters
   if (!is.null(additional_params)) {
-    assert_that(is.list(additional_params),
+    assertthat::assert_that(is.list(additional_params),
       msg = "Please provide 'additional_params' as a named list.
       See details for more information"
     )
     # Check additional parameters
     if (from == "cds") {
-      assert_that(names(additional_params) %in% c("reduction_method", "labels_exist", "align_pseudotime_method"),
+      assertthat::assert_that(names(additional_params) %in% c("reduction_method", "labels_exist", "align_pseudotime_method"),
         msg = "Allowed additional parameters for 'cds' (cds/CellDataSet) are
         'reduction_method', and 'labels_exist','align_pseudotime_method'."
       )
     } else if (from == "sce") {
-      assert_that(all(names(additional_params) %in% c("exist_ptime_col", "exist_path_col", "labels_exist")),
+      assertthat::assert_that(all(names(additional_params) %in% c("exist_ptime_col", "exist_path_col", "labels_exist")),
         msg = "Allowed additional parameters for sce are 'exist_ptime_col',
                   'exist_path_col', and 'labels_exist'."
       )

R/create_scmp.R

@@ -33,23 +33,33 @@ create_scmp <- function(counts,
                         path_col,
                         use_as_bin = FALSE) {
   # Validation Checks
-  assert_that(ncol(counts) == nrow(cell_data),
+  assertthat::assert_that(ncol(counts) == nrow(cell_data),
     msg = paste("Number of cells in raw-counts and cell-level-metadata are different.")
   )
 
-  assert_that(all(colnames(counts) == rownames(cell_data)),
+  assertthat::assert_that(all(colnames(counts) == rownames(cell_data)),
     msg = paste("Rownames of raw-counts and cell-level-metadata are different.")
   )
 
   if (!is.null(bin_counts) || !is.null(bin_cell_data)) {
-    assert_that(nrow(bin_counts) == nrow(bin_cell_data),
+    assertthat::assert_that(nrow(bin_counts) == nrow(bin_cell_data),
       msg = paste("Number of cells in bin_counts and bin_cell_data are different.")
     )
-    assert_that(all(rownames(bin_counts) == rownames(bin_cell_data)),
+    assertthat::assert_that(all(rownames(bin_counts) == rownames(bin_cell_data)),
       msg = paste("Rownames of bin_counts and bin_cell_data are different.")
     )
   }
 
+  # Validate if path_col is present in cell_data
+  assertthat::assert_that(path_col %in% colnames(cell_data),
+    msg = paste("Column name '", path_col, "' not found in cell_data.")
+  )
+
+  # Validate if ptime_col is present in cell_data
+  assertthat::assert_that(ptime_col %in% colnames(cell_data),
+    msg = paste("Column name '", ptime_col, "' not found in cell_data.")
+  )
+
   # Create Single-Cell Experiment Object
   sparse_tmp <- SingleCellExperiment(
     list(counts = counts),
@@ -61,7 +71,7 @@ create_scmp <- function(counts,
     Sparse = sparse_tmp,
     Dense = SingleCellExperiment(assays = list(bulk.counts = matrix(0, nrow = 0, ncol = 0)))
   )
-  sparse_tmp <- NULL
+  rm(sparse_tmp)
 
   # Use as bin
   if (use_as_bin) {
@@ -76,7 +86,7 @@ create_scmp <- function(counts,
 
     # Transfer Data
     scmpObj@Dense <- sparse_tmp
-    sparse_tmp <- NULL
+    rm(sparse_tmp)
 
     # Update the slots
     scmpObj@Parameters@bin_ptime_col <- ptime_col