Merge branch 'dev' of https://github.com/montilab/hypeR into dev

.travis.yml

@@ -10,6 +10,7 @@ env:
     - R_BUILD_ARGS="--no-build-vignettes --no-manual"
     - R_CHECK_ARGS="--no-build-vignettes --no-manual --timings"
     - _R_CHECK_TIMINGS_="0"
+    - R_DEFAULT_INTERNET_TIMEOUT="300"
 
 r:
   - release

R/ggeplot.R

@@ -10,22 +10,26 @@
 #' @importFrom ggplot2 qplot aes geom_rug geom_hline geom_vline annotate theme element_text element_blank element_line element_rect
 #' 
 #' @export
-ggeplot <- function(n, positions, x_axis, y_axis, title="") {
-    score <- which.max(abs(y_axis))
-    qplot(x_axis, 
-          y_axis,
-          main=title,
-          ylab="Running Enrichment Score", 
-          xlab="Position in Ranked List of Genes",
-          geom="line")+
-    geom_rug(data=data.frame(positions), aes(x=positions), inherit.aes=FALSE)+
-    geom_hline(yintercept=0) +
-    geom_vline(xintercept=n/2, linetype="dotted") +
-    annotate("point", x=x_axis[score], y=y_axis[score], color="red") +
-    annotate("text", x=x_axis[score]+n/20, y=y_axis[score], label=round(y_axis[score],2)) +
-    annotate("point", x=x_axis[score], y=y_axis[score], color="red") +
-    theme(plot.title=element_text(hjust=0.5),
-          panel.background=element_blank(), 
-          axis.line=element_line(color="black"),
-          panel.border=element_rect(color="black", fill=NA, size=1))    
+ggeplot <- function(n, positions, x_axis, y_axis, title = "") {
+  score <- which.max(abs(y_axis))
+  DF <- data.frame(x_axis = x_axis, y_axis = y_axis)
+  ggplot2::ggplot(DF, aes(x = x_axis, y = y_axis)) +
+    ggplot2::geom_line() +
+    ggplot2::labs(
+      title = title,
+      y = "Running Enrichment Score",
+      x = "Position in Ranked List of Genes"
+    ) +
+    ggplot2::geom_rug(data = data.frame(positions), aes(x = positions), inherit.aes = FALSE) +
+    ggplot2::geom_hline(yintercept = 0) +
+    ggplot2::geom_vline(xintercept = n / 2, linetype = "dotted") +
+    ggplot2::annotate("point", x = x_axis[score], y = y_axis[score], color = "red") +
+    ggplot2::annotate("text", x = x_axis[score] + n / 20, y = y_axis[score], label = round(y_axis[score], 2)) +
+    ggplot2::annotate("point", x = x_axis[score], y = y_axis[score], color = "red") +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(hjust = 0.5),
+      panel.background = ggplot2::element_blank(),
+      axis.line = ggplot2::element_line(color = "black"),
+      panel.border = ggplot2::element_rect(color = "black", fill = NA, linewidth = 1)
+    )
 }

R/ggvenn.R

@@ -37,7 +37,7 @@ ggvenn <- function(a, b, ga, gb, title="") {
                         paste(gb, " (", x.b, ")", sep=""))) %>%
 
     ggplot(aes(x0=x, y0=y, r=c(r.a, r.b), fill=groups)) +
-    geom_circle(alpha=0.3, size=0.5) +
+    geom_circle(alpha=0.3, linewidth=0.5) +
     coord_fixed() +
     theme_void() +
     theme(plot.title=element_text(hjust=0.5),

tests/testthat/test-hyp_to_table.R

@@ -1,22 +1,21 @@
 test_that("hyp_to_table() is working", {
+  testdat <- readRDS(file.path(system.file("extdata", package = "hypeR"), "testdat.rds"))
+  gsets_obj <- testdat$gsets
+  rgsets_obj <- testdat$rgsets
 
-    testdat <- readRDS(file.path(system.file("extdata", package="hypeR"), "testdat.rds"))
-    gsets_obj <- testdat$gsets
-    rgsets_obj <- testdat$rgsets
-
-    signature <- testdat$signature
-    experiment <- testdat$experiment
-
-    hyp_obj <- hypeR(signature, gsets_obj)
-    multihyp_obj <- hypeR(experiment, rgsets_obj)
-
-    # A single file
-    hyp_to_table(hyp_obj, file_path="signature.txt", sep="\t")
-    expect_true(file.exists("signature.txt"))
-
-    # Multiple files within a directory
-    hyp_to_table(multihyp_obj, file_path="experiment", sep="\t")
-    expect_true(file.exists("experiment/Signature 1.txt"))
-    expect_true(file.exists("experiment/Signature 2.txt"))
-    expect_true(file.exists("experiment/Signature 3.txt"))
+  signature <- testdat$signature
+  experiment <- testdat$experiment
+
+  hyp_obj <- hypeR(signature, gsets_obj)
+  multihyp_obj <- hypeR(experiment, rgsets_obj)
+
+  # A single file
+  hyp_to_table(hyp_obj, file_path = "signature.txt", sep = "\t")
+  expect_true(file.exists("signature.txt"))
+
+  # Multiple files within a directory
+  hyp_to_table(multihyp_obj, file_path = "experiment", sep = "\t")
+  expect_true(file.exists("experiment/Signature 1.txt"))
+  expect_true(file.exists("experiment/Signature 2.txt"))
+  expect_true(file.exists("experiment/Signature 3.txt"))
 })