Merge pull request #66 from UCLouvain-CBIO/issue55

Issue55

NEWS.md

@@ -2,6 +2,7 @@
 
 ## scp 1.15.2
 
+- fix: fixed x-axis direction annotation for volcano plot on contrast
 - fix: solved bug in DA when missing contrast level in modelled 
   feature (issue #65).
 

R/ScpModel-DifferentialAnalysis.R

@@ -601,11 +601,33 @@ scpVolcanoPlot <- function(differentialList,
         ylab("-log10(Adjusted p-value)") +
         theme_minimal()
     if (!is.null(contrast)) {
-        pl <- pl + xlab(paste(
-            contrast[[3]], " <-   log2(Fold change)   -> ",
-            contrast[[2]]
-        ))
+        pl <- pl + .annotateDirection(df$Estimate, contrast)
     }
     pl
 }
 
+## Internal function that generates an intuitively annotates the log
+## fold change axis. This is performed by highlighting the direction
+## of change for the two groups in the contrast. Note however that the
+## annotation is adapted in case that the changes are unidirectional.
+## Then, only the contrast group where intensities are estimated to be
+## higher is shown.
+##
+## The function returns an object of class "labels" that can be used
+## as the x axis for a ggplot fig.
+##
+## @param logFoldChange A numeric() containing estimated log fold
+##   changes.
+## @param contrast A `character(3)` with the following elements: 1.
+##   The name of a categorical variable to test; 2. The name of the
+##   reference group: 3. The name of the second group to contrast
+##   against the reference group. `coefficients` and `contrasts`
+##   cannot be both NULL.
+.annotateDirection <- function(logFoldChange, contrast) {
+    xAnnotation <- "log2(Fold change)"
+    if (any(logFoldChange > 0))
+        xAnnotation <- paste(xAnnotation, "  ->", contrast[[3]])
+    if (any(logFoldChange < 0))
+        xAnnotation <- paste(contrast[[2]], "<-  ", xAnnotation)
+    xlab(xAnnotation)
+}

R/ScpModel-Workflow.R

@@ -372,7 +372,7 @@ scpModelWorkflow <- function(object, formula,
 ##
 .fitModel <- function(y, x, effectNames) {
     model <- ScpModelFit(nrow(x), ncol(x))
-    if (!ncol(x)) return(model)
+    if (!ncol(x) || !nrow(x) || nrow(x) < ncol(x)) return(model)
     res <- .fitRidge(y[rownames(x)], x)
     scpModelFitCoefficients(model) <- res$coefficients
     scpModelFitResiduals(model) <- res$residuals

tests/testthat/test-ScpModel-DifferentialAnalysis.R

@@ -773,7 +773,7 @@ test_that("scpVolcanoPlot", {
                                            paste0("col", 1:100)))
     ))
     se$condition <- as.factor(rep(1:2, length.out = ncol(se)))
-    assay(se)[, se$condition == 2] <- rnorm(nrow(se)) + assay(se)[, se$condition == 2]
+    assay(se)[, se$condition == 2] <- 1:nrow(se) - nrow(se) / 2 + assay(se)[, se$condition == 2]
     set.seed(124)
     assay(se) <- assay(se) + rnorm(length(assay(se)))
     assay(se)[sample(1:length(assay(se)), length(assay(se))/2)] <- NA
@@ -920,3 +920,32 @@ test_that(".plotVolcano", {
                      textBy = "names", contrast = c("condition", "A", "B"))
     )
 })
+
+test_that(".annotateDirection", {
+    ## Annotate axis with 2 directions, that is logFoldChange contains
+    ## positive and negative values
+    expect_identical(
+        .annotateDirection(-10:10, c("Group", "foo", "bar")),
+        xlab("foo <-   log2(Fold change)   -> bar")
+    )
+    ## Reverse direction
+    expect_identical(
+        .annotateDirection(-10:10, c("Group", "bar", "foo")),
+        xlab("bar <-   log2(Fold change)   -> foo")
+    )
+    ## Only positive direction = right annotation
+    expect_identical(
+        .annotateDirection(10:0, c("Group", "foo", "bar")),
+        xlab("log2(Fold change)   -> bar")
+    )
+    ## Only negative direction = left annotation
+    expect_identical(
+        .annotateDirection(-10:0, c("Group", "foo", "bar")),
+        xlab("foo <-   log2(Fold change)")
+    )
+    ## Only zero = no direction annotation
+    expect_identical(
+        .annotateDirection(0, c("Group", "foo", "bar")),
+        xlab("log2(Fold change)")
+    )
+})