Fix lints

campbio · Apr 7, 2021 · 4e9b7ef · 4e9b7ef · lintr-bot · Apr 9, 2021
1 parent e01b013
commit 4e9b7ef
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Showing 6 changed files with 17 additions and 19 deletions.
diff --git a/R/celda_C.R b/R/celda_C.R
@@ -712,7 +712,7 @@ setMethod("celda_C",
 
   ## Maximization to find best label for each cell
   probs <- .countsTimesProbs(counts, phi) + theta[, s]
-  
+
   if (isTRUE(doSample)) {
     zPrevious <- z
     z <- apply(probs, 2, which.max)
@@ -945,11 +945,11 @@ setMethod("celda_C",
 .countsTimesProbs <- function(counts, phi) {
   ## Maximization to find best label for each cell
   if (inherits(counts, "matrix") & is.integer(counts)) {
-    probs <- eigenMatMultInt(phi, counts) 
+    probs <- eigenMatMultInt(phi, counts)
   } else if (inherits(counts, "matrix") & is.numeric(counts)) {
-    probs <- eigenMatMultNumeric(phi, counts) 
+    probs <- eigenMatMultNumeric(phi, counts)
   } else {
-    probs <- (t(phi) %*% counts) 
-  } 
+    probs <- (t(phi) %*% counts)
+  }
   return(probs)
-}
+}
diff --git a/R/celda_functions.R b/R/celda_functions.R
@@ -276,7 +276,7 @@ setMethod("compareCountMatrix",
         }
         celdaChecksum <- params(celdaMod)$countChecksum
         counts <- .processCounts(counts)
-        
+
         # Checksums are generated in celdaGridSearch and model after processing
         count.md5 <- .createCountChecksum(counts)
         res <- isTRUE(count.md5 == celdaChecksum)
@@ -329,7 +329,7 @@ setMethod("compareCountMatrix",
         }
         celdaChecksum <- celdaMod@countChecksum
         counts <- .processCounts(counts)
-        
+
         # Checksums are generated in celdaGridSearch and model after processing
         count.md5 <- .createCountChecksum(counts)
         res <- isTRUE(count.md5 == celdaChecksum)
@@ -442,10 +442,9 @@ distinctColors <- function(n,
 
 
 .processCounts <- function(counts) {
-  if(!((inherits(counts, "matrix") &
+  if (!((inherits(counts, "matrix") &
         (is.integer(counts) | is.numeric(counts))) |
-     inherits(counts, "dgCMatrix")))
-  {
+     inherits(counts, "dgCMatrix"))) {
     stop("'counts' must be a sparse dgCMatrix ",
          "from the 'Matrix' package or a matrix containing integer or numeric ",
          "values.")
@@ -460,7 +459,7 @@ distinctColors <- function(n,
 .validateCounts <- function(counts) {
   countRowSum <- rowSums(counts)
   countColSum <- colSums(counts)
-  
+
   if (sum(countRowSum == 0) > 0 | sum(countColSum == 0) > 0) {
     stop(
       "Each row and column of the count matrix must have at least",

diff --git a/R/factorizeMatrix.R b/R/factorizeMatrix.R
@@ -223,7 +223,7 @@ setMethod("factorizeMatrix", signature(x = "ANY", celdaMod = "celda_C"),
         beta <- params(celdaMod)$beta
         sampleLabel <- sampleLabel(celdaMod)
         s <- as.integer(sampleLabel)
-        
+
         p <- .cCDecomposeCounts(counts, s, z, K)
         mCPByS <- p$mCPByS
         nGByCP <- p$nGByCP

diff --git a/R/moduleHeatmap.R b/R/moduleHeatmap.R
@@ -366,10 +366,10 @@ setMethod("moduleHeatmap",
         filteredNormCounts[filteredNormCounts > trim[2]] <- trim[2]
     }
 
-    if(is.null(rowFontSize)) {
+    if (is.null(rowFontSize)) {
         rowFontSize <- min(200 / nrow(filteredNormCounts), 20)
     }
-    
+
     if (isTRUE(showModuleLabel)) {
         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,
             col = col,

diff --git a/R/recursiveSplit.R b/R/recursiveSplit.R
@@ -1343,7 +1343,7 @@ setMethod("recursiveSplitModule",
       verbose = FALSE
     )
     modelInitial@params$countChecksum <- countChecksum
-    
+
     currentL <- length(unique(celdaClusters(modelInitial)$y)) + 1
     overallY <- celdaClusters(modelInitial)$y
 

diff --git a/tests/testthat/test-celda_CG.R b/tests/testthat/test-celda_CG.R
@@ -58,7 +58,7 @@ test_that(desc = paste0("Testing simulateCells celda_CG, make sure all genes",
 
 # Ensure logLikelihood calculates the expected values
 test_that(desc = "Testing logLikelihood functions for celda_CG", {
-    expect_lt(logLikelihood(modelCG),0)
+    expect_lt(logLikelihood(modelCG), 0)
 
     fakeZ <- celdaClusters(modelCG)
     fakeZ[1] <- K + 1
@@ -211,5 +211,4 @@ test_that(desc = "Testing plotCeldaViolin with celda_CG", {
             "facet",
             "plot_env",
             "labels"))
-})
-
+})