style: make names camelCase for conformance with Bioconductor rules

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>

.lintr

@@ -4,7 +4,7 @@ linters: linters_with_tags(
     indentation_linter(indent = 4L, hanging_indent_style = "tidy"),
     undesirable_function_linter(modify_defaults(defaults = default_undesirable_functions, library = NULL)),
     object_usage_linter = NULL,
-    object_name_linter(styles = c("snake_case", "camelCase", "PascalCase", "dotted.case")))
+    object_name_linter(styles = c("camelCase")))
 encoding: "UTF-8"
 exclusions: list(
     "renv/activate.R",

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '.*\.(csv|tsv|xls)$'
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: v0.4.2
     hooks:
     -   id: use-tidy-description
     -   id: codemeta-description-updated
@@ -44,7 +44,7 @@ repos:
     -   id: no-debug-statement
     -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=500']
@@ -59,7 +59,7 @@ repos:
         -   --fix=no
     -   id: trailing-whitespace
 -   repo: https://github.com/compilerla/conventional-pre-commit
-    rev: v3.1.0
+    rev: v3.2.0
     hooks:
     -   args:
         -   build
@@ -78,7 +78,7 @@ repos:
         stages:
         -   commit-msg
 -   repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.5.4
+    rev: v1.5.5
     hooks:
     -   id: forbid-crlf
     -   id: remove-crlf

R/consensus_concordants.R

@@ -6,20 +6,20 @@
 #'
 #' @examples
 #' TRUE
-target_rename <- function(input_names) {
-    if ("treatment" %in% input_names) {
-        new_cols <- c(
+targetRename <- function(inputNames) {
+    if ("treatment" %in% inputNames) {
+        newCols <- c(
             "TargetSignature", "Target", "TargetCellLine",
             "TargetTime", "Similarity", "sig_direction"
         )
     } else {
-        new_cols <- c(
+        newCols <- c(
             "TargetSignature", "Target", "TargetCellLine",
             "TargetTime", "TargetConcentration", "Similarity", "sig_direction"
         )
     }
 
-    new_cols
+    newCols
 }
 
 #' Generate a Consensus list of Targets
@@ -48,10 +48,10 @@ target_rename <- function(input_names) {
 #'
 #' @examples
 #' TRUE
-consensus_concordants <- function(...,
-                                  paired = FALSE,
-                                  cutoff = 0.321,
-                                  cell_line = NULL) {
+consensusConcordants <- function(...,
+                                 paired = FALSE,
+                                 cutoff = 0.321,
+                                 cellLine = NULL) {
     if (paired && length(list(...)) != 2L) {
         stop("Paired analysis requires two data frames")
     } else if (!paired && length(list(...)) != 1L) {
@@ -60,9 +60,9 @@ consensus_concordants <- function(...,
 
     concordants <- dplyr::bind_rows(list(...))
 
-    if (!is.null(cell_line)) {
+    if (!is.null(cellLine)) {
         concordants <- concordants %>%
-            dplyr::filter(.data[["cellline"]] %in% cell_line)
+            dplyr::filter(.data[["cellline"]] %in% cellLine)
     }
 
     filtered <- concordants %>%
@@ -80,7 +80,7 @@ consensus_concordants <- function(...,
             ))
         ) %>%
         dplyr::arrange(dplyr::desc(abs(.data[["similarity"]]))) %>%
-        dplyr::rename_with(target_rename) %>%
+        dplyr::rename_with(targetRename) %>%
         dplyr::ungroup()
 
     filtered

R/filter_signature.R

@@ -27,8 +27,8 @@
 #'
 #' @examples
 #' TRUE
-filter_signature <- function(signature, direction = "any",
-                             threshold = NULL, prop = NULL) {
+filterSignature <- function(signature, direction = "any",
+                            threshold = NULL, prop = NULL) {
     stopifnot("data.frame" %in% class(signature))
 
     if (!is.null(threshold) && !is.null(prop)) {
@@ -42,17 +42,17 @@ filter_signature <- function(signature, direction = "any",
 
     if (!is.null(threshold)) {
         if (length(threshold) == 2L) {
-            down_threshold <- threshold[[1L]]
-            up_threshold <- threshold[[2L]]
+            downThreshold <- threshold[[1L]]
+            upThreshold <- threshold[[2L]]
         } else if (length(threshold) == 1L) {
-            down_threshold <- -threshold
-            up_threshold <- threshold
+            downThreshold <- -threshold
+            upThreshold <- threshold
         } else {
             stop("Threshold must be specified as one or two values")
         }
     } else if (!is.null(prop)) {
-        down_threshold <- quantile(signature[["Value_LogDiffExp"]], prop)
-        up_threshold <- quantile(signature[["Value_LogDiffExp"]], 1.0 - prop)
+        downThreshold <- quantile(signature[["Value_LogDiffExp"]], prop)
+        upThreshold <- quantile(signature[["Value_LogDiffExp"]], 1.0 - prop)
     }
 
     if (direction == "up") {

R/get_concordants.R

@@ -28,28 +28,28 @@
 #'
 #' @examples
 #' TRUE
-get_concordants <- function(signature, ilincs_library = "CP",
-                            sig_direction = NULL) {
+getConcordants <- function(signature, ilincsLibrary = "CP",
+                           sigDirection = NULL) {
     if (!"data.frame" %in% class(signature)) {
         stop("signature must be a data frame or data frame like object")
     } else {
-        signature_file <- tempfile(pattern = "ilincs_sig", fileext = ".xls")
+        signatureFile <- tempfile(pattern = "ilincs_sig", fileext = ".xls")
         signature %>%
-            readr::write_tsv(signature_file)
+            readr::write_tsv(signatureFile)
     }
 
-    lib_map <- c(
+    libMap <- c(
         OE = "LIB_11",
         KD = "LIB_6",
         CP = "LIB_5"
     )
 
-    if (!ilincs_library %in% c("OE", "KD", "CP")) {
+    if (!ilincsLibrary %in% c("OE", "KD", "CP")) {
         stop("library must be one of 'OE', 'KD' or 'CP'")
     }
 
     url <- "http://www.ilincs.org/api/SignatureMeta/uploadAndAnalyze"
-    query <- list(lib = lib_map[ilincs_library])
+    query <- list(lib = libMap[ilincsLibrary])
     body <- list(file = httr::upload_file(signature_file))
 
     request <- httr::POST(url, query = query, body = body)
@@ -65,7 +65,7 @@ get_concordants <- function(signature, ilincs_library = "CP",
             dplyr::mutate(
                 similarity = round(.data[["similarity"]], 8L),
                 pValue = round(.data[["pValue"]], 20L),
-                sig_direction = sig_direction
+                sig_direction = sigDirection
             )
         return(concordants)
     } else {

R/get_signature.R

@@ -17,16 +17,16 @@
 #'
 #' @examples
 #' TRUE
-get_signature <- function(sig_id, l1000 = TRUE) {
+getSignature <- function(sigId, l1000 = TRUE) {
     url <- "http://www.ilincs.org/api/ilincsR/downloadSignature"
 
     if (l1000) {
-        num_genes <- 978L
+        numGenes <- 978L
     } else {
-        num_genes <- 25000L
+        numGenes <- 25000L
     }
 
-    query <- list(sigID = sig_id, noOfTopGenes = num_genes)
+    query <- list(sigID = sigId, noOfTopGenes = numGenes)
 
     request <- httr::POST(url, query = query)
 

R/investigate_signature.R

@@ -37,96 +37,96 @@
 #'
 #' @examples
 #' TRUE
-investigate_signature <- function(expr,
-                                  output_lib,
-                                  filter_threshold = NULL,
-                                  filter_prop = NULL,
-                                  similarity_threshold = 0.2,
-                                  paired = TRUE,
-                                  output_cell_lines = NULL,
-                                  gene_column = "Symbol",
-                                  logfc_column = "logFC",
-                                  pval_column = "PValue",
-                                  source_name = "Input",
-                                  source_cell_line = "NA",
-                                  source_time = "NA",
-                                  source_concentration = "NA") {
+investigateSignature <- function(expr,
+                                 outputLib,
+                                 filterThreshold = NULL,
+                                 filterProp = NULL,
+                                 similarityThreshold = 0.2,
+                                 paired = TRUE,
+                                 outputCellLines = NULL,
+                                 geneColumn = "Symbol",
+                                 logfcColumn = "logFC",
+                                 pvalColumn = "PValue",
+                                 sourceName = "Input",
+                                 sourceCellLine = "NA",
+                                 sourceTime = "NA",
+                                 sourceConcentration = "NA") {
     libs <- c("OE", "KD", "CP")
 
-    if (!output_lib %in% libs) {
+    if (!outputLib %in% libs) {
         stop("Output library must be one of 'OE', 'KD', 'CP'")
     }
 
-    if (missing(output_lib)) {
+    if (missing(outputLib)) {
         stop("Please specify an output library")
     }
 
-    expr_signature <- expr %>%
-        prepare_signature(
-            gene_column = gene_column,
-            logfc_column = logfc_column,
-            pval_column = pval_column
+    exprSignature <- expr %>%
+        prepareSignature(
+            gene_column = geneColumn,
+            logfc_column = logfcColumn,
+            pval_column = pvalColumn
         )
 
-    signature_id <- unique(expr_signature[["signatureID"]])
+    signatureId <- unique(exprSignature[["signatureID"]])
 
     if (paired) {
-        filtered_up <- expr_signature %>%
-            filter_signature(
+        filteredUp <- exprSignature %>%
+            filterSignature(
                 direction = "up",
-                threshold = filter_threshold,
-                prop = filter_prop
+                threshold = filterThreshold,
+                prop = filterProp
             )
 
-        filtered_down <- expr_signature %>%
-            filter_signature(
+        filteredDown <- exprSignature %>%
+            filterSignature(
                 direction = "down",
-                threshold = filter_threshold,
-                prop = filter_prop
+                threshold = filterThreshold,
+                prop = filterProp
             )
 
-        concordant_up <- filtered_up %>%
-            get_concordants(ilincs_library = output_lib, sig_direction = "Up")
+        concordantUp <- filteredUp %>%
+            getConcordants(ilincs_library = outputLib, sig_direction = "Up")
 
-        concordant_down <- filtered_down %>%
-            get_concordants(ilincs_library = output_lib, sig_direction = "Down")
+        concordantDown <- filteredDown %>%
+            getConcordants(ilincs_library = outputLib, sig_direction = "Down")
 
 
-        consensus_targets <-
-            consensus_concordants(
-                concordant_up,
-                concordant_down,
+        consensusTargets <-
+            consensusConcordants(
+                concordantUp,
+                concordantDown,
                 paired = paired,
-                cell_line = output_cell_lines,
-                cutoff = similarity_threshold
+                cell_line = outputCellLines,
+                cutoff = similarityThreshold
             )
     } else {
-        filtered <- expr_signature %>%
-            filter_signature(
+        filtered <- exprSignature %>%
+            filterSignature(
                 direction = "any",
-                threshold = filter_threshold,
-                prop = filter_prop
+                threshold = filterThreshold,
+                prop = filterProp
             )
 
         concordants <- filtered %>%
-            get_concordants(ilincs_library = output_lib)
+            getConcordants(ilincs_library = outputLib)
 
-        consensus_targets <-
-            consensus_concordants(
+        consensusTargets <-
+            consensusConcordants(
                 concordants,
                 paired = paired,
-                cell_line = output_cell_lines,
-                cutoff = similarity_threshold
+                cell_line = outputCellLines,
+                cutoff = similarityThreshold
             )
     }
 
-    augmented <- consensus_targets %>%
+    augmented <- consensusTargets %>%
         dplyr::mutate(
-            SourceSignature = signature_id,
-            Source = source_name,
-            SourceCellLine = source_cell_line,
-            SourceTime = source_time,
-            InputSignatureDirection = sig_direction
+            SourceSignature = signatureId,
+            Source = sourceName,
+            SourceCellLine = sourceCellLine,
+            SourceTime = sourceTime,
+            InputSignatureDirection = sigDirection
         ) %>%
         dplyr::select(
             dplyr::any_of(c(