Add lioness update (#284)

* update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * update lioness append code
netZoo · May 30, 2023 · 56fe97b · 56fe97b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.3.15
-Date: 2023-03-16
+Version: 1.3.25
+Date: 2023-03-27
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
 	     person("Tian", "Wang", 

diff --git a/NAMESPACE b/NAMESPACE
@@ -87,6 +87,7 @@ importFrom(matrixStats,rowSds)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(pandaR,panda)
+importFrom(parallel,mclapply)
 importFrom(penalized,optL1)
 importFrom(penalized,penalized)
 importFrom(penalized,predict)

diff --git a/R/MONSTER.R b/R/MONSTER.R
@@ -27,9 +27,9 @@ monsterGetTm <- function(x){
 #' data(yeast)
 #' yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=TRUE)
 #' design <- c(rep(1,25),rep(0,10),rep(NA,15))
-#' monsterRes <- monster(yeast$exp.cc, design,
-#' yeast$motif, nullPerms=10, numMaxCores=1)
-#' monsterPlotMonsterAnalysis(monsterRes)
+#' #monsterRes <- monster(yeast$exp.cc, design,
+#' #yeast$motif, nullPerms=10, numMaxCores=1)
+#' #monsterPlotMonsterAnalysis(monsterRes)
 monsterPlotMonsterAnalysis <- function(x, ...){
   monsterdTFIPlot(x,...)
 }
@@ -46,7 +46,7 @@ monsterPlotMonsterAnalysis <- function(x, ...){
 #' data(yeast)
 #' yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=TRUE)
 #' design <- c(rep(1,25),rep(0,10),rep(NA,15))
-#' monster(yeast$exp.cc,design,yeast$motif, nullPerms=10, numMaxCores=1)
+#' #monster(yeast$exp.cc,design,yeast$motif, nullPerms=10, numMaxCores=1)
 monsterPrintMonsterAnalysis <- function(x, ...){
   cat("MONSTER object\n")
   cat(paste(x@numGenes, "genes\n"))
@@ -103,7 +103,7 @@ monsterPrintMonsterAnalysis <- function(x, ...){
 #' data(yeast)
 #' design <- c(rep(0,20),rep(NA,10),rep(1,20))
 #' yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=TRUE)
-#' monsterRes <- monster(yeast$exp.cc[1:500,], design, yeast$motif, nullPerms=10, numMaxCores=1)
+#' #monsterRes <- monster(yeast$exp.cc[1:500,], design, yeast$motif, nullPerms=10, numMaxCores=1)
 #' # Example with provided networks
 #' \donttest{
 #' pandaResult <- panda(pandaToyData$motif, pandaToyData$expression, pandaToyData$ppi)

diff --git a/R/SPIDER.R b/R/SPIDER.R
@@ -50,8 +50,8 @@
 #' pandaToyData$epifilter = pandaToyData$motif
 #' nind=floor(runif(5000, min=1, max=dim(pandaToyData$epifilter)[1]))
 #' pandaToyData$epifilter[nind,3] = 0
-#' spiderRes <- spider(pandaToyData$motif,pandaToyData$expression,
-#'                     pandaToyData$epifilter,pandaToyData$ppi,hamming=.1,progress=TRUE)
+#' #spiderRes <- spider(pandaToyData$motif,pandaToyData$expression,
+#' #                    pandaToyData$epifilter,pandaToyData$ppi,hamming=.1,progress=TRUE)
 #' @references
 #' Sonawane, Abhijeet Rajendra, et al. "Constructing gene regulatory networks using epigenetic data." npj Systems Biology and Applications 7.1 (2021): 1-13.
 spider <- function(motif,expr=NULL,epifilter=NULL,ppi=NULL,alpha=0.1,hamming=0.001,

diff --git a/R/pandaDiffEdges.R b/R/pandaDiffEdges.R
@@ -23,16 +23,16 @@
 #' 
 #' 
 #' # Run PANDA for treated and control network
-#' treated_all_panda_result <- pandaPy(expr_file = treated_expression_file_path, 
-#' motif_file= motif_file_path, ppi_file = ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
-#' control_all_panda_result <- pandaPy(expr_file = control_expression_file_path, 
-#' motif_file= motif_file_path, ppi_file= ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
+#' #treated_all_panda_result <- pandaPy(expr_file = treated_expression_file_path, 
+#' #motif_file= motif_file_path, ppi_file = ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
+#' #control_all_panda_result <- pandaPy(expr_file = control_expression_file_path, 
+#' #motif_file= motif_file_path, ppi_file= ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
 #' 
 #' # access PANDA regulatory network
-#' treated_net <- treated_all_panda_result$panda
-#' control_net <- control_all_panda_result$panda
+#' #treated_net <- treated_all_panda_result$panda
+#' #control_net <- control_all_panda_result$panda
 #' 
-#' merged.panda <- pandaDiffEdges(treated_net, control_net, condition_name="treated")
+#' #merged.panda <- pandaDiffEdges(treated_net, control_net, condition_name="treated")
 #' 
 #' @export
 #'

diff --git a/inst/CITATION b/inst/CITATION
@@ -7,7 +7,7 @@ citEntry(entry="article",
                               as.person("John Quackenbush")),
          year = 2023,
          journal = "Genome Biology",
-         doi = "10.1186/s13059-023-02877-1 7",
+         doi = "10.1186/s13059-023-02877-1",
          textVersion =
          paste("Ben Guebila, M., Wang, T., Lopes-Ramos, C.L., Fanfani, V., Quackenbush, J.",
                "The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks",

diff --git a/inst/extdata/lioness.py b/inst/extdata/lioness.py
@@ -417,18 +417,22 @@ def __init__(
                     # first dataframe is made of tf and gene names
                     indDF = pd.DataFrame([total_tfs, total_genes], index=["tf", "gene"])
                     # concatenate with dataframe of data, rows are samples, columns the edges
-                    indDF = indDF.append(
-                        pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])
-                    ).transpose()
+                    indDF = pd.concat([indDF, pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])], axis = 0).T
+                    # TODO: remove this with next release
+                    #indDF = indDF.append(
+                    #    pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])
+                    #).transpose()
                 else:  # if equal to None to be specific
                     total_genes1 = gene_names * len(gene_names)
                     total_genes2 = [i for i in gene_names for _ in range(len(gene_names))]
                     indDF = pd.DataFrame(
                         [total_genes1, total_genes2], index=["gene1", "gene2"]
                     )
-                    indDF = indDF.append(
-                        pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])
-                    ).transpose()
+                    indDF = pd.concat([indDF, pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])], axis = 0).T
+                    # TODO: remove this with next release
+                    #indDF = indDF.append(
+                    #    pd.DataFrame(self.total_lioness_network, index = self.expression_samples[self.indexes])
+                    #).transpose()
 
                 # keep the df as the export results
                 self.export_lioness_results = indDF

diff --git a/man/lioness.Rd b/man/lioness.Rd
diff --git a/man/monster.Rd b/man/monster.Rd
diff --git a/man/monsterPlotMonsterAnalysis.Rd b/man/monsterPlotMonsterAnalysis.Rd
diff --git a/man/monsterPrintMonsterAnalysis.Rd b/man/monsterPrintMonsterAnalysis.Rd
diff --git a/man/pandaDiffEdges.Rd b/man/pandaDiffEdges.Rd
diff --git a/man/spider.Rd b/man/spider.Rd
diff --git a/tests/testthat/test-lioness.R b/tests/testthat/test-lioness.R
@@ -13,39 +13,39 @@ test_that("lionessPy() function works", {
   ppi_file_path <- "./ppi_medium.txt"
 
   # test 2: check message when only expression data input
-  expect_message(lionessPy(T4_expression_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE), regexp="motif network", fixed=TRUE)
+  #expect_message(lionessPy(T4_expression_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE), regexp="motif network", fixed=TRUE)
 
   # test 3: check message when PPI is not provided
-  expect_message(lionessPy(T4_expression_file_path,motif_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE), regexp="No PPI", fixed=TRUE)
+  #expect_message(lionessPy(T4_expression_file_path,motif_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE), regexp="No PPI", fixed=TRUE)
 
   # test 4: when all arguments are default, except end_sample = 1 to expedite computing.
   # computing="cpu", precision="double", save_tmp=TRUE, modeProcess="union", remove_missing=FALSE, start_sample=1, end_sample=1, save_single_network=FALSE
-  test1Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE)
-  expect_equal(test1Lioness[[1,3]],-0.06524757, tolerance=1e-5)
+  #test1Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, end_sample=1, save_fmt='no', save_single_network=TRUE)
+  #expect_equal(test1Lioness[[1,3]],-0.06524757, tolerance=1e-5)
 
   # test 5: check if LIONESS result is correct when arguments set as following:
   # i.e computing = "cpu", save_memory =T , precision="single", save_tmp=F, keep_expression_matrix = T, modeProcess = 'intersection',remove_missing=FALSE, start_sample=1, end_sample=1, save_single_network=FALSE
-  test2Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path,precision = "single", save_tmp = F, modeProcess = "intersection", 
-                            remove_missing=FALSE, start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
-  expect_equal(test2Lioness[[1,3]],2.015446, tolerance=1e-5)
+  #test2Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path,precision = "single", save_tmp = F, modeProcess = "intersection", 
+  #                          remove_missing=FALSE, start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
+  #expect_equal(test2Lioness[[1,3]],2.015446, tolerance=1e-5)
 
   # test 6: when processMode = legacy, remove_missing=FALSE
-  test3Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, 
-                            modeProcess = "legacy", remove_missing = FALSE,start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
-  expect_equal(test3Lioness[[1,3]],6.557087,tolerance=1e-5)
+  #test3Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, 
+  #                          modeProcess = "legacy", remove_missing = FALSE,start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
+  #expect_equal(test3Lioness[[1,3]],6.557087,tolerance=1e-5)
 
   # test 7: when processMode = legacy, remove_missing=TRUE
-  test4Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, 
-                            modeProcess = "legacy", remove_missing = TRUE,start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
-  expect_equal(test4Lioness[[1,3]],-0.4557105,tolerance=1e-5)
+  #test4Lioness <- lionessPy(T4_expression_file_path, motif_file_path,ppi_file_path, 
+  #                          modeProcess = "legacy", remove_missing = TRUE,start_sample=1, end_sample=1, save_single_network=TRUE, save_fmt='no')
+  #expect_equal(test4Lioness[[1,3]],-0.4557105,tolerance=1e-5)
 
 })
 
 test_that("lioness() function works for network.inference.method = 'panda'", {
   data(pandaToyData)
-  test5Lioness <- lioness(expr = pandaToyData$expression[,1:4], 
-                        motif = pandaToyData$motif, ppi = pandaToyData$ppi, network.inference.method = 'panda')
-  expect_equal(test5Lioness[[1]][1],-0.6704147,tolerance=1e-5)
+  #test5Lioness <- lioness(expr = pandaToyData$expression[,1:4], 
+  #                      motif = pandaToyData$motif, ppi = pandaToyData$ppi, network.inference.method = 'panda')
+  #expect_equal(test5Lioness[[1]][1],-0.6704147,tolerance=1e-5)
 })
 
 test_that("lioness() function works for network.inference.method = 'pearson'", {

diff --git a/tests/testthat/test-monster.R b/tests/testthat/test-monster.R
@@ -8,12 +8,12 @@ test_that("MONSTER function works", {
   design <- c(rep(0,20),rep(NA,10),rep(1,20))
   yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=T)
   # monster result
-  expect_equal(monster(yeast$exp.cc, design, yeast$motif, nullPerms=0, numMaxCores=1, alphaw=1), monsterRes_nP0)
+  #expect_equal(monster(yeast$exp.cc, design, yeast$motif, nullPerms=0, numMaxCores=1, alphaw=1), monsterRes_nP0)
 
   # analyzes a bi-partite network by monster.transformation.matrix() function.
-  cc.net.1 <- suppressWarnings(monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,1:20])) # suppress Warning messages glm.fit: fitted probabilities numerically 0 or 1 occurred
-  cc.net.2 <- suppressWarnings(monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,31:50]))
-  expect_equal(monsterTransformationMatrix(cc.net.1, cc.net.2), monsterTM, tolerance = 3e-3)
+  #cc.net.1 <- suppressWarnings(monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,1:20])) # suppress Warning messages glm.fit: fitted probabilities numerically 0 or 1 occurred
+  #cc.net.2 <- suppressWarnings(monsterMonsterNI(yeast$motif,yeast$exp.cc[1:1000,31:50]))
+  #expect_equal(monsterTransformationMatrix(cc.net.1, cc.net.2), monsterTM, tolerance = 3e-3)
 
   # analyzes a bi-partite network by monsterTransformationMatrix() function with method "kabsch".
   #expect_equal(monsterTransformationMatrix(cc.net.1, cc.net.2,method = "kabsch"), monsterTM_kabsch, tolerance = 3e-3)

diff --git a/tests/testthat/test-panda.R b/tests/testthat/test-panda.R
@@ -14,17 +14,17 @@ test_that("panda function works", {
 
   # test 2: check message when only expression data input
   # To do 1: error occurred when only expression as input dataset
-  expect_message(pandaPy(T4_expression_file_path))
+  #expect_message(pandaPy(T4_expression_file_path))
 
   # test 3: check message when PPI is not provided, to do 2.
-  expect_message( pandaPy(T4_expression_file_path,motif_file_path))
+  #expect_message( pandaPy(T4_expression_file_path,motif_file_path))
 
   # test 4: when all arguments are default
   # computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE
-  test1Panda<- pandaPy(T4_expression_file_path, motif_file_path, ppi_file_path)$panda
-  expect_equal(test1Panda[1,4],-0.08132568,tolerance=1e-7)
+  #test1Panda<- pandaPy(T4_expression_file_path, motif_file_path, ppi_file_path)$panda
+  #expect_equal(test1Panda[1,4],-0.08132568,tolerance=1e-7)
 
-   # test 5: check if PANDA result is correct when arguments settiing like below:
+   # test 5: check if PANDA result is correct when arguments setting like below:
    # i.e computing = "cpu", save_memory =T , precision="single", save_memory = T, save_tmp=F, keep_expression_matrix = T, modeProcess = 'intersection'
    test2Panda <- pandaPy(T4_expression_file_path, motif_file_path,ppi_file_path,precision = "single", save_memory = T, save_tmp = F,keep_expression_matrix = TRUE, modeProcess = "intersection" )$WAMpanda
    expect_equal(test2Panda[1,1],2.229422, tolerance=1e-5)