From ef8318e7711ce3bfd4933a9ffb0239af3dddd759 Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Thu, 31 Aug 2023 10:09:04 -0400
Subject: [PATCH 1/6] bug corrected: ggeplot --> ggplot

---
 R/ks_enrichment.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ks_enrichment.R b/R/ks_enrichment.R
index 88dfc1f..f6b84cd 100644
--- a/R/ks_enrichment.R
+++ b/R/ks_enrichment.R
@@ -83,7 +83,7 @@
   
   # Enrichment plot
   p <- if (plotting) {
-    ggeplot(n.x, y, x.axis, y.axis, plot.title) + 
+    ggplot2::ggplot(n.x, y, x.axis, y.axis, plot.title) + 
       geom_vline(xintercept=leading_edge, linetype="dotted", color="red", size=0.25)
   }
   else ggempty()

From 03b05bb4da2b25221fe983e2731ce115c12ef21e Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Thu, 31 Aug 2023 10:12:47 -0400
Subject: [PATCH 2/6] mistaken correction reverted: ggplot --> ggeplot

---
 R/ks_enrichment.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ks_enrichment.R b/R/ks_enrichment.R
index f6b84cd..88dfc1f 100644
--- a/R/ks_enrichment.R
+++ b/R/ks_enrichment.R
@@ -83,7 +83,7 @@
   
   # Enrichment plot
   p <- if (plotting) {
-    ggplot2::ggplot(n.x, y, x.axis, y.axis, plot.title) + 
+    ggeplot(n.x, y, x.axis, y.axis, plot.title) + 
       geom_vline(xintercept=leading_edge, linetype="dotted", color="red", size=0.25)
   }
   else ggempty()

From 68649b863be211e41d8011dd02c03a738777bcd6 Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Fri, 15 Sep 2023 11:46:24 -0400
Subject: [PATCH 3/6] reconciled handling of leading edge

---
 R/ks_enrichment.R | 134 ++++++++++++++++++++++------------------------
 1 file changed, 65 insertions(+), 69 deletions(-)

diff --git a/R/ks_enrichment.R b/R/ks_enrichment.R
index 88dfc1f..33dd637 100644
--- a/R/ks_enrichment.R
+++ b/R/ks_enrichment.R
@@ -21,17 +21,15 @@
                     plot.title="") 
 {
   n.y <- length(y)
-  err = list(score=0, pval=1, leading_edge=NULL, leading_hits=NA, plot=ggempty())
-
-  if (n.y < 1 ) return(err)
-  if (any(y > n.x)) return(err)
-  if (any(y < 1)) return(err)
-  
+  err <- list(score = 0, pval = 1, leading_edge = NULL, leading_hits = NULL, plot = ggempty())
+  if (n.y < 1 || any(y > n.x) || any(y < 1) ) {
+    return(err)
+  }
   x.axis <- y.axis <- NULL
   leading_edge <- NULL # recording the x corresponding to the highest y value
   
-  # If weights are provided
-  if (!is.null(weights)) {
+  ## If weights are provided
+  if ( !is.null(weights) ) {
     weights <- abs(weights[y])^weights.pwr
     
     Pmis <- rep(1, n.x); Pmis[y] <- 0; Pmis <- cumsum(Pmis); Pmis <- Pmis/(n.x-n.y)
@@ -42,9 +40,9 @@
     
     x.axis <- 1:n.x
     y.axis <- z
-    
-    # Without weights
-  } else {
+  } 
+  ## Without weights
+  else {
     y <- sort(y)
     n <- n.x*n.y/(n.x + n.y)
     hit <- 1/n.y
@@ -57,7 +55,7 @@
     D[y.match] <- (1:n.y)
     zero <- which(D == 0)[-1]
     D[zero] <- D[zero-1]
-
+    
     z <- D*hit-Y*mis
     
     score <- if (absolute) max(z)-min(z) else z[leading_edge <- which.max(abs(z))]
@@ -75,24 +73,26 @@
     }    
   }
   leading_edge <- x.axis[leading_edge]
-  leading_hits <- intersect(x.axis[x.axis<=leading_edge],y)
+  leading_hits <- intersect(x.axis[x.axis <= leading_edge], y)
   
-  # One-sided Kolmogorov–Smirnov test
+  ## One-sided Kolmogorov–Smirnov test
   results <- suppressWarnings(ks.test(1:n.x, y, alternative="less"))
   results$statistic <- score  # Use the signed statistic
   
-  # Enrichment plot
-  p <- if (plotting) {
-    ggeplot(n.x, y, x.axis, y.axis, plot.title) + 
-      geom_vline(xintercept=leading_edge, linetype="dotted", color="red", size=0.25)
+  ## Enrichment plot
+  p <- if (plotting && n.y > 0) {
+    ggeplot(n.x, y, x.axis, y.axis, plot.title) +
+      geom_vline(xintercept = leading_edge, linetype = "dotted", color = "red", size = 0.25)
+  } else {
+    ggempty()
   }
-  else ggempty()
-  
-  return(list(score=as.numeric(results$statistic), 
-              pval=results$p.value, 
-              leading_edge=leading_edge,
-              leading_hits=leading_hits,
-              plot=p))
+  return(list(
+    score = as.numeric(results$statistic),
+    pval = results$p.value,
+    leading_edge = leading_edge,
+    leading_hits = leading_hits,
+    plot = p
+  ))
 }
 #' Enrichment test via one-sided Kolmogorov–Smirnov test
 #' 
@@ -105,66 +105,62 @@
 #' @return A list of data and plots
 #' 
 #' @keywords internal
-.ks_enrichment <- function(signature,
-                           genesets,
-                           weights=NULL,
-                           weights.pwr=1,
-                           absolute=FALSE,
-                           plotting=TRUE) 
+.ks_enrichment <- function(
+    signature,
+    genesets,
+    weights = NULL,
+    weights.pwr = 1,
+    absolute = FALSE,
+    plotting = TRUE) 
 {
   if (!is(genesets, "list")) stop("Error: Expected genesets to be a list of gene sets\n")
   if (!is.null(weights)) stopifnot(length(signature) == length(weights))
-  
+
   signature <- unique(signature)
   genesets <- lapply(genesets, unique)
-  
-  results <- mapply(function(geneset, title) {
-    
+
+  results <- mapply( function(geneset, title) {
     ranks <- match(geneset, signature)
     ranks <- ranks[!is.na(ranks)]
 
     ## Run ks-test
-    results <- .kstest(n.x=length(signature), 
-                         y=ranks,
-                         weights=weights,
-                         weights.pwr=weights.pwr,
-                         absolute=absolute, 
-                         plotting=plotting,
-                         plot.title=title)
-    
-    results[['geneset']] <- length(geneset)
-    edge_idx <- results[['leading_edge']]
+    results_in <- .kstest(
+      n.x = length(signature),
+      y = ranks,
+      weights = weights,
+      weights.pwr = weights.pwr,
+      absolute = absolute,
+      plotting = plotting,
+      plot.title = title
+    )
+    #results_in[["geneset"]] <- length(geneset)
+    results_in[["geneset"]] <- length(intersect(geneset, signature))
+    results_in[["overlap"]] <- length(results_in$leading_hits)
+    return(results_in)
+  }, genesets, names(genesets), USE.NAMES = TRUE, SIMPLIFY = FALSE)
 
-    if(is.null(edge_idx)) {
-      results[['hits']] <- NA
-      results[['overlap']] <- 0
-    } else if (!is.null(edge_idx) & edge_idx == 0) {
-      results[['hits']] <- NA
-      results[['overlap']] <- 0
-    } else {
-      results[['hits']] <- paste0("'", signature[results[['leading_hits']]], "'", collapse=',')
-      results[['overlap']] <- edge_idx
-    }
-    return(results)
-    
-  }, genesets, names(genesets), USE.NAMES=TRUE, SIMPLIFY=FALSE)
-  
   results <- do.call(rbind, results)
-  data <- data.frame(apply(results[,c("score", "pval", "geneset", "overlap")], 2, unlist), 
-                     stringsAsFactors = FALSE)
+  data <- data.frame(apply(results[, c("score", "pval", "geneset", "overlap")], 2, unlist),
+    stringsAsFactors = FALSE
+  )
   ## add list of genes in the leading edge
-  data$hits <- results[,"hits"]
+  data <- data %>%
+    dplyr::mutate(hits = sapply(results[, "leading_hits"], function(x) paste(signature[x], collapse = ",")))
   data$score <- signif(data$score, 2)
   data$pval <- signif(data$pval, 2)
   data$label <- names(genesets)
   data$signature <- length(signature)
-  data$fdr <- signif(p.adjust(data$pval, method="fdr"), 2)
+  data$fdr <- signif(p.adjust(data$pval, method = "fdr"), 2)
   data <- data %>%
-    dplyr::relocate(fdr,.after=pval) %>%
-    dplyr::relocate(signature,.after=geneset) %>%
-    dplyr::relocate(label)
-  plots <- results[,"plot"]
+    dplyr::relocate(fdr, .after = pval) %>%
+    dplyr::relocate(signature, .after = geneset) %>%
+    dplyr::relocate(label) |>
+    tibble::remove_rownames() # make sure this is OK
+  plots <- results[, "plot"]
 
-  return(list(data=data, 
-              plots=plots))
+  return(list(
+    data = data,
+    plots = plots,
+    leading_hits = sapply(results[, "leading_hits"], function(x) signature[x])
+  ))
 }

From 4a489fc115da92e4ed910586059aa8c3d5ad3f3f Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Fri, 15 Sep 2023 13:47:11 -0400
Subject: [PATCH 4/6] multiple edits, including split of hits by
 space-comma-space

---
 R/ggeplot.R                        | 40 +++++++++++----------
 R/ggvenn.R                         |  2 +-
 R/ks_enrichment.R                  |  5 +--
 tests/testthat/test-hyp_to_table.R | 37 ++++++++++---------
 tests/testthat/test-hype.R         | 57 ++++++++++++++++--------------
 5 files changed, 75 insertions(+), 66 deletions(-)

diff --git a/R/ggeplot.R b/R/ggeplot.R
index 779a648..c46c484 100644
--- a/R/ggeplot.R
+++ b/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)
+    )
 }
diff --git a/R/ggvenn.R b/R/ggvenn.R
index 60964eb..3853330 100644
--- a/R/ggvenn.R
+++ b/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),
diff --git a/R/ks_enrichment.R b/R/ks_enrichment.R
index 33dd637..93ce0e7 100644
--- a/R/ks_enrichment.R
+++ b/R/ks_enrichment.R
@@ -82,7 +82,7 @@
   ## Enrichment plot
   p <- if (plotting && n.y > 0) {
     ggeplot(n.x, y, x.axis, y.axis, plot.title) +
-      geom_vline(xintercept = leading_edge, linetype = "dotted", color = "red", size = 0.25)
+      geom_vline(xintercept = leading_edge, linetype = "dotted", color = "red", linewidth = 0.25)
   } else {
     ggempty()
   }
@@ -145,7 +145,8 @@
   )
   ## add list of genes in the leading edge
   data <- data %>%
-    dplyr::mutate(hits = sapply(results[, "leading_hits"], function(x) paste(signature[x], collapse = ",")))
+    #dplyr::mutate(hits = sapply(results[, "leading_hits"], function(x) paste(signature[x], collapse = ",")))
+    dplyr::mutate(hits = sapply(results[, "leading_hits"], function(x) paste(signature[x], collapse = " , ")))
   data$score <- signif(data$score, 2)
   data$pval <- signif(data$pval, 2)
   data$label <- names(genesets)
diff --git a/tests/testthat/test-hyp_to_table.R b/tests/testthat/test-hyp_to_table.R
index dd8d69e..b34a17b 100644
--- a/tests/testthat/test-hyp_to_table.R
+++ b/tests/testthat/test-hyp_to_table.R
@@ -1,22 +1,21 @@
 test_that("hyp_to_table() is working", {
+  testdat <- readRDS(file.path(system.file("extdata", package = "hypeR"), "testdat.rds"))
+  gsets_obj <- testdat$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"))
 })
diff --git a/tests/testthat/test-hype.R b/tests/testthat/test-hype.R
index 4f7db97..f5e0cae 100644
--- a/tests/testthat/test-hype.R
+++ b/tests/testthat/test-hype.R
@@ -15,23 +15,23 @@ hyp_tests <- function(hyp_obj, test_plots=FALSE, return_obj=FALSE) {
 hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets_obj) {
 
     # Basic
-    hypeR(signature, genesets, test=test, background=2520) %>%
+    hypeR(signature, genesets, test=test, background=2520) |>
     hyp_tests()    
             
     # Basic
-    hypeR(signature, gsets_obj, test=test, background=2520) %>%
+    hypeR(signature, gsets_obj, test=test, background=2520) |>
     hyp_tests()
     
     # Basic with plots
-    hypeR(signature, gsets_obj, test=test, background=2520, plotting=TRUE) %>%
+    hypeR(signature, gsets_obj, test=test, background=2520, plotting=TRUE) |>
     hyp_tests(test_plots=TRUE)
     
     # Test pval_cutoff
-    hypeR(signature, gsets_obj, test=test, background=100, pval=0.0001) %>%
+    hypeR(signature, gsets_obj, test=test, background=100, pval=0.0001) |>
     hyp_tests()
     
     # Test fdr_cutoff
-    hyp_obj <- hypeR(signature, gsets_obj, test=test, background=100, fdr=0.0001) %>%
+    hyp_obj <- hypeR(signature, gsets_obj, test=test, background=100, fdr=0.0001) |>
                hyp_tests(return_obj=TRUE)
     
     expect_equal(hyp_obj$args$genesets, gsets_obj)
@@ -39,7 +39,7 @@ hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets
     expect_equal(hyp_obj$args$fdr, 0.0001)
     
     # Test relational gsets
-    hyp_obj <- hypeR(signature, rgsets_obj, test=test, background=80, pval=0.01) %>%
+    hyp_obj <- hypeR(signature, rgsets_obj, test=test, background=80, pval=0.01) |>
                hyp_tests(return_obj=TRUE)
     expect_is(hyp_obj$args$genesets, "rgsets")
     expect_is(hyp_obj$args$genesets, "R6")
@@ -51,17 +51,17 @@ hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets
     expect_equal(names(multihyp_obj$data), c("Signature 1", "Signature 2", "Signature 3"))
     
     # Extracting hyp objects
-    multihyp_obj$data[["Signature 1"]] %>%
+    multihyp_obj$data[["Signature 1"]] |>
     hyp_tests()
     
     # Extracting hyp objects with plots
     multihyp_obj <- hypeR(experiment, gsets_obj, test=test, background=100, plotting=TRUE)
-    multihyp_obj$data[["Signature 1"]] %>%
+    multihyp_obj$data[["Signature 1"]] |>
     hyp_tests(test_plots=TRUE)
     
     # Test relational gsets
     multihyp_obj <- hypeR(experiment, rgsets_obj, test=test, background=100, pval=0.05)
-    multihyp_obj$data[["Signature 2"]] %>%
+    multihyp_obj$data[["Signature 2"]] |>
     hyp_tests()
 }
 
@@ -89,44 +89,49 @@ test_that("Hypergeometric is working", {
     
     # Hypergeometric
     hyp_obj <- hypeR(s, gs, background=length(bg))
-    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, gs$G1, length(bg)))
-    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, gs$G2, length(bg)))
-    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, gs$G3, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, gs$G1, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, gs$G2, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, gs$G3, length(bg)))
     
     # Hypergeometric - Restrict Genesets to Background
     hyp_obj <- hypeR(s, gs, background=bg[1:18])
-    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
     
     gsets_obj <- gsets$new(gs, quiet=TRUE)   
     hyp_obj <- hypeR(s, gsets_obj, background=bg[1:18])
-    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
 })
 
 test_that("KS Test is working", {
 
   genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")$genesets[1:5]
-  all_genes <- genesets %>% unlist %>% unname
+  all_genes <- genesets |> unlist(use.names = FALSE)
   genesets_names <- names(genesets)
 
-  experiment <- c(head(genesets[[1]], 5), LETTERS, tail(genesets[[1]], 1))
-
   # Geneset 1 is top skewed
+  experiment <- c(head(genesets[[1]], 5), LETTERS, tail(genesets[[1]], 1))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  expect_equal(hyp_obj$data[genesets_names[[1]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[1]][1:5], "'",collapse=","))
-
+  #expect_equal(hyp_obj$data[genesets_names[[1]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[1]][1:5], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[1]]) |> dplyr::pull(hits) |> unname(), 
+               paste(genesets[[1]][1:5], collapse = " , "))
+  
   # Geneset 2 is mixed
   experiment <- c(head(genesets[[2]], 8), LETTERS, tail(genesets[[2]], 10))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  expect_equal(hyp_obj$data[genesets_names[[2]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[2]][1:8], "'",collapse=","))
-
+  #expect_equal(hyp_obj$data[genesets_names[[2]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[2]][1:8], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[2]]) |> dplyr::pull(hits) |> unname(), 
+               paste(genesets[[2]][1:8], collapse = " , "))
+  
   # Geneset 3 is bottom skewed
   experiment <- c(head(genesets[[3]], 1), LETTERS, tail(genesets[[3]], 8))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  expect_equal(hyp_obj$data[genesets_names[[3]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[3]][1], "'",collapse=","))
+  #expect_equal(hyp_obj$data[genesets_names[[3]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[3]][1], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[3]]) |> dplyr::pull(hits) |> unname(), 
+               paste(genesets[[3]][1], collapse = " , "))
 })
 
 test_that("hypeR() is working", {

From 46f5859fe589f119b53e0b55f1d1c7fe14a2b637 Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Fri, 15 Sep 2023 14:18:27 -0400
Subject: [PATCH 5/6] tried to increase internet timeout

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index b5f80e3..4e19cc8 100644
--- a/.travis.yml
+++ b/.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

From 73b639a98506d8d6f6d8b32440828aef25f981a2 Mon Sep 17 00:00:00 2001
From: tetomonti <montilab@bu.edu>
Date: Fri, 15 Sep 2023 15:10:55 -0400
Subject: [PATCH 6/6] switched |> to %>% for backward compatibility

---
 R/ks_enrichment.R          |  2 +-
 tests/testthat/test-hype.R | 50 +++++++++++++++++++-------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/R/ks_enrichment.R b/R/ks_enrichment.R
index 93ce0e7..0a4aad9 100644
--- a/R/ks_enrichment.R
+++ b/R/ks_enrichment.R
@@ -155,7 +155,7 @@
   data <- data %>%
     dplyr::relocate(fdr, .after = pval) %>%
     dplyr::relocate(signature, .after = geneset) %>%
-    dplyr::relocate(label) |>
+    dplyr::relocate(label) %>%
     tibble::remove_rownames() # make sure this is OK
   plots <- results[, "plot"]
 
diff --git a/tests/testthat/test-hype.R b/tests/testthat/test-hype.R
index f5e0cae..485d310 100644
--- a/tests/testthat/test-hype.R
+++ b/tests/testthat/test-hype.R
@@ -15,23 +15,23 @@ hyp_tests <- function(hyp_obj, test_plots=FALSE, return_obj=FALSE) {
 hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets_obj) {
 
     # Basic
-    hypeR(signature, genesets, test=test, background=2520) |>
+    hypeR(signature, genesets, test=test, background=2520) %>%
     hyp_tests()    
             
     # Basic
-    hypeR(signature, gsets_obj, test=test, background=2520) |>
+    hypeR(signature, gsets_obj, test=test, background=2520) %>%
     hyp_tests()
     
     # Basic with plots
-    hypeR(signature, gsets_obj, test=test, background=2520, plotting=TRUE) |>
+    hypeR(signature, gsets_obj, test=test, background=2520, plotting=TRUE) %>%
     hyp_tests(test_plots=TRUE)
     
     # Test pval_cutoff
-    hypeR(signature, gsets_obj, test=test, background=100, pval=0.0001) |>
+    hypeR(signature, gsets_obj, test=test, background=100, pval=0.0001) %>%
     hyp_tests()
     
     # Test fdr_cutoff
-    hyp_obj <- hypeR(signature, gsets_obj, test=test, background=100, fdr=0.0001) |>
+    hyp_obj <- hypeR(signature, gsets_obj, test=test, background=100, fdr=0.0001) %>%
                hyp_tests(return_obj=TRUE)
     
     expect_equal(hyp_obj$args$genesets, gsets_obj)
@@ -39,7 +39,7 @@ hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets
     expect_equal(hyp_obj$args$fdr, 0.0001)
     
     # Test relational gsets
-    hyp_obj <- hypeR(signature, rgsets_obj, test=test, background=80, pval=0.01) |>
+    hyp_obj <- hypeR(signature, rgsets_obj, test=test, background=80, pval=0.01) %>%
                hyp_tests(return_obj=TRUE)
     expect_is(hyp_obj$args$genesets, "rgsets")
     expect_is(hyp_obj$args$genesets, "R6")
@@ -51,17 +51,17 @@ hypeR_tests <- function(test, signature, experiment, genesets, gsets_obj, rgsets
     expect_equal(names(multihyp_obj$data), c("Signature 1", "Signature 2", "Signature 3"))
     
     # Extracting hyp objects
-    multihyp_obj$data[["Signature 1"]] |>
+    multihyp_obj$data[["Signature 1"]] %>%
     hyp_tests()
     
     # Extracting hyp objects with plots
     multihyp_obj <- hypeR(experiment, gsets_obj, test=test, background=100, plotting=TRUE)
-    multihyp_obj$data[["Signature 1"]] |>
+    multihyp_obj$data[["Signature 1"]] %>%
     hyp_tests(test_plots=TRUE)
     
     # Test relational gsets
     multihyp_obj <- hypeR(experiment, rgsets_obj, test=test, background=100, pval=0.05)
-    multihyp_obj$data[["Signature 2"]] |>
+    multihyp_obj$data[["Signature 2"]] %>%
     hyp_tests()
 }
 
@@ -89,48 +89,48 @@ test_that("Hypergeometric is working", {
     
     # Hypergeometric
     hyp_obj <- hypeR(s, gs, background=length(bg))
-    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, gs$G1, length(bg)))
-    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, gs$G2, length(bg)))
-    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, gs$G3, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, gs$G1, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, gs$G2, length(bg)))
+    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, gs$G3, length(bg)))
     
     # Hypergeometric - Restrict Genesets to Background
     hyp_obj <- hypeR(s, gs, background=bg[1:18])
-    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
     
     gsets_obj <- gsets$new(gs, quiet=TRUE)   
     hyp_obj <- hypeR(s, gsets_obj, background=bg[1:18])
-    expect_equal(filter(hyp_obj$data, label == "G1") |> pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G2") |> pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
-    expect_equal(filter(hyp_obj$data, label == "G3") |> pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G1") %>% pull(pval), fisher(s, intersect(gs$G1, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G2") %>% pull(pval), fisher(s, intersect(gs$G2, bg[1:18]), length(bg[1:18])))
+    expect_equal(filter(hyp_obj$data, label == "G3") %>% pull(pval), fisher(s, intersect(gs$G3, bg[1:18]), length(bg[1:18])))
 })
 
 test_that("KS Test is working", {
 
   genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")$genesets[1:5]
-  all_genes <- genesets |> unlist(use.names = FALSE)
+  all_genes <- genesets %>% unlist(use.names = FALSE)
   genesets_names <- names(genesets)
 
   # Geneset 1 is top skewed
   experiment <- c(head(genesets[[1]], 5), LETTERS, tail(genesets[[1]], 1))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  #expect_equal(hyp_obj$data[genesets_names[[1]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[1]][1:5], "'",collapse=","))
-  expect_equal(filter(hyp_obj$data, label == genesets_names[[1]]) |> dplyr::pull(hits) |> unname(), 
+  #expect_equal(hyp_obj$data[genesets_names[[1]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[1]][1:5], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[1]]) %>% dplyr::pull(hits) %>% unname(), 
                paste(genesets[[1]][1:5], collapse = " , "))
   
   # Geneset 2 is mixed
   experiment <- c(head(genesets[[2]], 8), LETTERS, tail(genesets[[2]], 10))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  #expect_equal(hyp_obj$data[genesets_names[[2]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[2]][1:8], "'",collapse=","))
-  expect_equal(filter(hyp_obj$data, label == genesets_names[[2]]) |> dplyr::pull(hits) |> unname(), 
+  #expect_equal(hyp_obj$data[genesets_names[[2]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[2]][1:8], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[2]]) %>% dplyr::pull(hits) %>% unname(), 
                paste(genesets[[2]][1:8], collapse = " , "))
   
   # Geneset 3 is bottom skewed
   experiment <- c(head(genesets[[3]], 1), LETTERS, tail(genesets[[3]], 8))
   hyp_obj <- hypeR(experiment, genesets, background=2522, test="kstest")
-  #expect_equal(hyp_obj$data[genesets_names[[3]], "hits"] |> unlist(use.names=FALSE), paste0("'", genesets[[3]][1], "'",collapse=","))
-  expect_equal(filter(hyp_obj$data, label == genesets_names[[3]]) |> dplyr::pull(hits) |> unname(), 
+  #expect_equal(hyp_obj$data[genesets_names[[3]], "hits"] %>% unlist(use.names=FALSE), paste0("'", genesets[[3]][1], "'",collapse=","))
+  expect_equal(filter(hyp_obj$data, label == genesets_names[[3]]) %>% dplyr::pull(hits) %>% unname(), 
                paste(genesets[[3]][1], collapse = " , "))
 })