Merge branch 'master' into modify-terminalStateFromMarkovChain-

.github/workflows/R-CMD-check.yml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest }
-          # - { os: macos-latest } # disabling until https://github.com/r-lib/actions/issues/950 is resolved
+          - { os: macos-latest } # disabling until https://github.com/r-lib/actions/issues/950 is resolved
           - { os: windows-latest }
     runs-on: ${{ matrix.config.os }}
     env:
@@ -60,7 +60,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
-          packages: any::covr
 
       - uses: r-lib/actions/check-r-package@v2
 
@@ -80,6 +79,12 @@ jobs:
       - name: Debug permissions output
         run: |
           echo "Has permission: ${{ steps.check_permissions.outputs.has_permission }}"
+          
+      - name: Setup to test coverage
+        uses: r-lib/actions/setup-r-dependencies@v2
+        if: steps.check_permissions.outputs.has_permission == 'true' && matrix.config.os == 'ubuntu-latest'
+        with:
+          packages: covr
 
       - name: Test coverage
         if: steps.check_permissions.outputs.has_permission == 'true' && matrix.config.os == 'ubuntu-latest'

R/markovProbability.R

@@ -62,16 +62,16 @@ markovProbability <- function(
     diffusiontime = NULL, pseudotime_key = "pseudotime", scale_components = TRUE,
     num_waypoints = 500) {
     if (is.null(milo[[pseudotime_key]])) {
-        if (is.null(diffusiontime)) {
+        if (is.null(diffusiontime)) { # nocov start
             abort(paste(
                 "Missing pseudotime data. This data can be either stored in",
                 deparse(substitute(milo)), "or provided by parameter diffusiontime"
-            ))
+            )) # nocov end
         } else {
             milo[[pseudotime_key]] <- diffusiontime
         }
     } else {
-        diffusiontime <- milo[[pseudotime_key]]
+        diffusiontime <- milo[[pseudotime_key]] # nocov
     }
 
     # scale data
@@ -98,7 +98,7 @@ markovProbability <- function(
     colnames(new_coldata) <- c(names(terminal_state))
     # prevent same name in colData
     idx <- names(colData(milo)) %in% colnames(new_coldata)
-    if (any(idx)) {
+    if (any(idx)) { # nocov start
         warning(paste(
             "Name", paste(names(colData(milo))[idx], collapse = ", "),
             "already exists in", as.character(substitute(milo))
@@ -121,7 +121,7 @@ markovProbability <- function(
                 message("Invalid response. Please enter 'y' or 'n'.")
             }
         }
-    }
+    } # nocov end
     colData(milo) <- cbind(colData(milo), new_coldata)
     return(milo)
 }

R/setupVdjPseudobulk.R

@@ -112,22 +112,22 @@ setupVdjPseudobulk <- function(
         abort(paste(
             "ValueError: length of check_vj_mapping should be 2. But", length(check_vj_mapping),
             "was provided."
-        ))
+        )) # nocov
     }
     .typeCheck(check_vdj_mapping, "logical")
     if (length(check_vdj_mapping) != 3) {
         abort(paste(
             "ValueError: length of check_vj_mapping should be 3. But", length(check_vdj_mapping),
             "was provided."
-        ))
+        )) # nocov
     }
     .typeCheck(check_extract_cols_mapping, "character")
     .typeCheck(remove_missing, "logical")
 
     # filtering retain only productive entries based on specified mode
     if (!already.productive) {
         if (is.null(mode_option)) {
-            if (!is.null(productive_cols)) {
+            if (!is.null(productive_cols)) { # nocov start
                 msg <- paste(productive_cols, collapse = ", ")
                 message(sprintf("Checking productivity from %s ..."), appendLF = FALSE)
                 cnumber0 <- dim(sce)[2]
@@ -140,7 +140,7 @@ setupVdjPseudobulk <- function(
                 message(sprintf("%d of cells filtered", filtered))
             } else {
                 abort("When mode_option is NULL, the productive_cols must be specified.")
-            }
+            } # nocov end
         } else {
             produ_col <- paste("productive", mode_option, c("VDJ", "VJ"), sep = "_")[c(
                 productive_vdj,
@@ -195,8 +195,8 @@ setupVdjPseudobulk <- function(
     if (is.null(extract_cols)) {
         message("Parameter extract_cols do not provided, automatically geneterate colnames for extraction.")
         if (!length(grep("_VDJ_main|_VJ_main", names(colData(sce))))) {
-            v_call <- if ("v_call_genotyped_VDJ" %in% colnames(colData(sce))) {
-                "v_call_genotyped_"
+            v_call <- if ("v_call_genotyped_VDJ" %in% colnames(colData(sce))) { # nocov start
+                "v_call_genotyped_" # nocov end
             } else {
                 "v_call_"
             }
@@ -211,12 +211,12 @@ setupVdjPseudobulk <- function(
                     "d_call_", mode_option,
                     "_VJ"
                 )]
-            } else {
+            } else { # nocov start
                 suffix <- c("VDJ", "VJ")
                 extr_cols <- as.vector(outer(prefix, suffix, function(x, y) {
                     paste0(x, y)
                 }))
-                extr_cols <- extr_cols[extr_cols != paste0("d_call_", "VJ")]
+                extr_cols <- extr_cols[extr_cols != paste0("d_call_", "VJ")] # nocov end
             }
             msg <- paste(extr_cols, collapse = ", ")
             message(sprintf("Detect whether colData %s already exist...", msg))
@@ -228,7 +228,7 @@ setupVdjPseudobulk <- function(
                         "Keyerror: Automatically generated colnames's length is",
                         length(extr_cols), ".It must have the same number with the vdj data columns, which is",
                         length(splitVdj[[1]]), "\nYou could use parameter extract_cols to specify the columns to match the length"
-                    ))
+                    )) # nocov
                 } else {
                     vdj <- lapply(seq(length(extr_cols)), function(X, sc) {
                         vapply(X = sc, "[", X, FUN.VALUE = character(1))
@@ -241,7 +241,7 @@ setupVdjPseudobulk <- function(
                     "Keyerror: Automatically generated colnames", paste0(extr_cols[!extr_cols %in%
                         colnames(colData(sce))], collapse = ", "), "must be contained in colData",
                     "\nYou could use parameter extract_cols to specify the columns to extract TCR"
-                ))
+                )) # nocov
             }
             message(sprintf("Extract main TCR from %s ...", msg), appendLF = FALSE)
             sce <- Reduce(function(data, ex_col) {
@@ -255,7 +255,7 @@ setupVdjPseudobulk <- function(
             }, extr_cols, init = sce)
             message("Complete.")
         }
-    } else {
+    } else { # nocov start
         msg <- paste(extract_cols, collapse = ", ")
         if (!any(extract_cols %in% colnames(colData(sce)))) {
             message(sprintf(
@@ -294,7 +294,7 @@ setupVdjPseudobulk <- function(
             data
         }, extract_cols, init = sce)
         message("Complete.")
-    }
+    } # nocov end
     # remove unclear mapping
     if (filter_unmapped) {
         filter_pattern <- ",|None|No_contig"
@@ -315,7 +315,7 @@ setupVdjPseudobulk <- function(
                 ))
             }
         } else {
-            if (is.null(extract_cols)) {
+            if (is.null(extract_cols)) { # nocov start
                 if (any(check_vdj_mapping)) {
                     vdj_mapping <- c("v_call", "d_call", "j_call")
                     extr_cols <- c(extr_cols, paste(vdj_mapping[check_vdj_mapping],
@@ -333,7 +333,7 @@ setupVdjPseudobulk <- function(
                 if (!is.null(check_extract_cols_mapping)) {
                     extr_cols <- check_extract_cols_mapping
                 }
-            }
+            } # nocov end
         }
         if (!is.null(extr_cols)) {
             msg <- paste(extr_cols, collapse = ", ")

R/splitCTgene.R

@@ -45,10 +45,10 @@ formatVdj <- function(gene_list) {
 chainAssign <- function(vec, num) {
     if (length(vec) == (num + 1)) {
         chains <- vec[seq_len(num)]
-    } else if (all(vec == "NA")) {
+    } else if (all(vec == "NA")) { # nocov start
         chains <- rep("None", num)
     } else {
-        abort
+        abort # nocov end
     }
     return(chains)
 }
@@ -64,16 +64,16 @@ chainAssign <- function(vec, num) {
             # Check if all elements are also lists
             all_are_lists <- TRUE
             for (item in sublist) {
-                if (!is.list(item)) {
+                if (!is.list(item)) { # nocov start
                     all_are_lists <- FALSE
                     break
-                }
+                } # nocov end
             }
             # If all elements are lists, unlist one level
             if (all_are_lists) {
                 return(unlist(sublist, recursive = FALSE))
             }
         }
-        return(sublist)
+        return(sublist) # nocov
     })
 }

R/terminalStateFromMarkovChain.R

@@ -1,4 +1,4 @@
-#' .terminalStateFromMarkovChain
+#' Determine terminal states using Markov chain if terminal states are not provided.
 #'
 #' @param Transmat Transition matrix
 #' @param wp_data Multi scale data of the waypoints
@@ -11,8 +11,8 @@
 #' @importFrom spam nearest.dist
 #' @return terminal_state
 .terminalStateFromMarkovChain <- function(Transmat, wp_data, pseudotime, waypoints) {
-    message("No terminal state provided, indentification of terminal states....")
-    # Identify terminal states dm_boudaries
+    message("No terminal state provided, identification of terminal states....")
+    # Identify terminal states dm_boundaries
     n <- min(dim(Transmat))
     ei <- eigen(t(Transmat))
     idx <- order(Re(ei$values), decreasing = TRUE)[seq_len(10)]
@@ -26,7 +26,7 @@
         stats::median(ranks))))
     # connect components of cells beyond cutoff
     cells <- which(ranks > cutoff)
-    # Find connected componets
+    # Find connected components
     graph <- graph_from_adjacency_matrix(Transmat[cells, cells],
         weighted = TRUE,
         mode = "directed"

R/vdjPseudobulk.R

@@ -66,14 +66,14 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
                           ), col_to_take = NULL, normalise = TRUE, renormalise = FALSE, min_count = 1L) {
     # type check
     if (!is(milo, "Milo") && !is(milo, "SingleCellExperiment")) {
-        abort("Uncompatible data type, \nmilo msut be either Milo or SingleCellExperiment object")
+        abort("Uncompatible data type, \nmilo msut be either Milo or SingleCellExperiment object") # nocov
     }
     .classCheck(pbs, "Matrix")
     if (!all(col_to_bulk %in% names(colData(milo)))) {
-        abort("Inappropriate argument value: \nocol_to_bulk should within the name of coldata of milo")
+        abort("Inappropriate argument value: \nocol_to_bulk should within the name of coldata of milo") # nocov
     }
     if (!all(col_to_take %in% names(colData(milo)))) {
-        abort("Inappropriate argument value: \ncol_to_take should within the name of coldata of milo")
+        abort("Inappropriate argument value: \ncol_to_take should within the name of coldata of milo") # nocov
     }
     .typeCheck(normalise, "logical")
     .typeCheck(renormalise, "logical")
@@ -88,9 +88,9 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
     } else {
         pbs <- .getPbs(pbs, col_to_bulk, milo)
     }
-    # set the column used in caculation
+    # set the column used in calculation
     if (is.null(extract_cols)) {
-        if (is.null(mode_option)) {
+        if (is.null(mode_option)) { # nocov start
             all.col.n <- colnames(colData(milo))
             extract_cols <- all.col.n[grep("_call_VDJ_main|_call_VJ_main", all.col.n)]
         } else {
@@ -99,7 +99,7 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
                 mode_option, "_VDJ_main|", mode_option,
                 "_call_VJ_main"
             ), all.col.n)]
-        }
+        } # nocov end
     }
     # perform matrix multiplication of pseudobulks by cell matrix by a cells by
     # VJs matrix strat off by creating the cell by VJs matix skip the prefix
@@ -110,7 +110,7 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
         if (!is.factor(x)) {
             as.factor(x)
         } else {
-            x
+            x # nocov
         }
     })
     requireNamespace("stats")
@@ -139,7 +139,7 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
             defined.min.counts <- define.count >= min_count
             # normalise the pseudobulks
             pseudo_vdj_feature[, group.define.mask] <- pseudo_vdj_feature[, group.define.mask] / define.count
-            if (renormalise) {
+            if (renormalise) { # nocov start
                 redefine.count <- apply(
                     pseudo_vdj_feature[defined.min.counts, group.define.mask],
                     1, sum
@@ -148,7 +148,7 @@ vdjPseudobulk <- function(milo, pbs = NULL, col_to_bulk = NULL, extract_cols = c
                     defined.min.counts,
                     group.define.mask
                 ] / define.count
-            }
+            } # nocov end
             pseudo_vdj_feature[!defined.min.counts, group.define.mask] <- 0
         }
     }