From e92cb6e068a47e6e65d71e7501e09b8a377c02d1 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Tue, 16 Aug 2022 14:00:16 -0400 Subject: [PATCH] update pandapy with header argument --- DESCRIPTION | 2 +- NAMESPACE | 1 + R/PANDA.R | 13 +- docs/404.html | 7 +- docs/CONDUCT.html | 7 +- docs/LICENSE-text.html | 7 +- docs/articles/ALPACA.html | 10 +- docs/articles/ApplicationinGTExData.html | 11 +- docs/articles/ApplicationwithTBdataset.html | 11 +- .../figure-html/unnamed-chunk-8-1.png | Bin 875796 -> 876338 bytes docs/articles/CONDOR.html | 33 +- .../figure-html/unnamed-chunk-10-1.png | Bin 28992 -> 31051 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 46162 -> 44738 bytes docs/articles/EGRET_toy_example.html | 9 +- .../LionessApplicationinGTExData.html | 35 +- .../figure-html/unnamed-chunk-6-1.png | Bin 205334 -> 206398 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 221789 -> 232908 bytes docs/articles/MONSTER.html | 497 +- .../figure-html/unnamed-chunk-10-1.png | Bin 299980 -> 307614 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docs/reference/sambarCorgenelength.html | 7 +- docs/reference/sambarDesparsify.html | 7 +- docs/reference/small1976.html | 7 +- docs/reference/sourcePPI.html | 13 +- docs/reference/visPandaInCytoscape.html | 19 +- docs/reference/yeast.html | 7 +- inst/extdata/panda.py | 367 +- man/lionessPy.Rd | 2 +- man/pandaDiffEdges.Rd | 55 + man/pandaPy.Rd | 3 +- 117 files changed, 19218 insertions(+), 889 deletions(-) create mode 100644 man/pandaDiffEdges.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 29593462..83ae821f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: netZooR Type: Package Title: Unified methods for the inference and analysis of gene regulatory networks -Version: 1.1.15 +Version: 1.1.16 Date: 2022-07-07 Authors@R: c(person("Marouen", "Ben Guebila", email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")), diff --git a/NAMESPACE b/NAMESPACE index b73dc999..29f527a0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -31,6 +31,7 @@ export(monsterTransitionNetworkPlot) export(monsterTransitionPCAPlot) export(monsterdTFIPlot) export(otter) +export(pandaDiffEdges) export(pandaPy) export(pandaToAlpaca) export(pandaToCondorObject) diff --git a/R/PANDA.R b/R/PANDA.R index 40f9c3f3..976a32fe 100644 --- a/R/PANDA.R +++ b/R/PANDA.R @@ -65,7 +65,7 @@ #' -pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE){ +pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE, with_header=FALSE){ if(missing(expr_file)){ stop("Please provide the path of gene expression data file to 'expr_file' variable") } @@ -106,6 +106,13 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", keepexpression.str <- "keep_expression_matrix=True" } else{ keepexpression.str <- "keep_expression_matrix=False" } + # with header option + if(with_header==FALSE){ + withheader.str <- "with_header=False" + }else if (with_header==TRUE){ + withheader.str <- "with_header=True" + } + # when pre-processing mode is legacy if(modeProcess == "legacy"){ @@ -130,7 +137,9 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", reticulate::source_python(pandapath,convert = TRUE) # invoke Python script to create a Panda object - obj.str <- paste("panda_obj=Panda(", expr.str, ",", motif.str,",", ppi.str, ",", computing.str, ",", precision.str, ",", savememory.str, ",", savetmp.str, "," , keepexpression.str, ",", mode.str, ")", sep ='') + obj.str <- paste("panda_obj=Panda(", expr.str, ",", motif.str,",", ppi.str, ",", + computing.str, ",", precision.str, ",", savememory.str, ",", savetmp.str, "," , + keepexpression.str, ",", mode.str, "," , withheader.str, ")", sep ='') # run Python code py_run_string(obj.str) diff --git a/docs/404.html b/docs/404.html index 40cee443..8ddfd96c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ netZooR - 1.0.4 + 1.1.16 @@ -130,6 +130,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization + +
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