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GRaNIEdev: Resolving all current issues and updated website

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src/GRaNIEdev/DESCRIPTION
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Package: GRaNIEdev
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.13.11
Version: 0.14.0
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
......
src/GRaNIEdev/NEWS.md
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<!--
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-->
# GRaNIE Changelog and News
# GRaNIEdev Changelog and News
## GRaNIEdev 0.9 - 0.11 (2021-06-24)
## GRaNIEdev 0.9 - 0.14 (2021-12-13)
### Major changes
- major overhaul and continuous work on peak-gene QC plots
- the *filterData* functions has now more filter parameters, such as filtering for CV. Also, all filters uniformly have a *min* and *max* filter.
- integrated network statistics and various enrichment analyses
- handling of edge cases and rare events in various functions
- packages have been renamed to *GRaNIE* as basename (before: *GRN*)
### Bug fixes
......
src/GRaNIEdev/R/plot.R
View file @ 214f1b28
......@@ -7,11 +7,12 @@
#' @template GRN
#' @template outputFolder
#' @param type Character. Either "peaks" or "rna" or "all". Type of data to plot a PCA for. "peaks" corresponds to the the open chromatin data, while "rna" refers to the RNA-seq counts. If set to "all", PCA will be done for both data modalities. In any case, PCA will be based on the original provided data before any additional normalization has been run (i.e., usually the raw data).
#' @param topn Integer vector. Default c(500,1000,5000). Number of top variable features to do PCA for. Can be a vector of different numbers (see default).
#' @template forceRerun
#' @return The same \code{\linkS4class{GRN}} object, without modifications. In addition, for each specified \code{type}, a PDF file is produced with a PCA. We refer to the Vignettes for details and further explanations.
#' @examples GRN = plotPCA_all(GRN, type = c("rna", "peaks"), forceRerun = TRUE)
#' @export
plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), forceRerun = FALSE) {
plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), topn = c(500,1000,5000), forceRerun = FALSE) {
GRN = .addFunctionLogToObject(GRN)
......@@ -66,7 +67,7 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), for
" RNA data for all shared samples to file ", fileCur ,
"... This may take a few minutes"))
.plot_PCA_wrapper(GRN, matrixCur, transformation = transformationCur, logTransformDensity = logTransformDensity, file = fileCur)
.plot_PCA_wrapper(GRN, matrixCur, transformation = transformationCur, logTransformDensity = logTransformDensity, file = fileCur, topn = topn)
} else {
futile.logger::flog.info(paste0("File ", fileCur, " already exists, not overwriting due to forceRerun = FALSE"))
......@@ -111,7 +112,7 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), for
" peaks data for all shared samples to file ", fileCur ,
"... This may take a few minutes"))
.plot_PCA_wrapper(GRN, matrixCur, transformation = transformationCur, logTransformDensity = logTransformDensity, file = fileCur)
.plot_PCA_wrapper(GRN, matrixCur, transformation = transformationCur, logTransformDensity = logTransformDensity, file = fileCur, topn = topn)
} else {
futile.logger::flog.info(paste0("File ", fileCur, " already exists, not overwriting due to forceRerun = FALSE"))
......@@ -129,10 +130,10 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), for
}
.plot_PCA_wrapper <- function(GRN, counts, transformation = "vst", scale = TRUE, logTransformDensity, fileCur) {
.plot_PCA_wrapper <- function(GRN, counts, transformation = "vst", scale = TRUE, logTransformDensity, fileCur, topn) {
checkmate::assertChoice(transformation, c("vst", "log2", "none"))
checkmate::assertIntegerish(topn, lower = 50, any.missing = FALSE,min.len = 1)
if (transformation == "vst") {
checkmate::assertClass(counts, "DESeqDataSet")
......@@ -165,7 +166,7 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), for
# 0. Density plot for ALL features
.plotDensity(counts.transf, logTransform = logTransformDensity)
for (topn in c(500,1000, 5000)) {
for (topn in topn) {
# select the ntop genes by variance
select <- order(rv, decreasing=TRUE)[seq_len(min(topn, length(rv)))]
......@@ -2057,7 +2058,7 @@ plotGeneralGraphStats <- function(GRN, outputFolder = NULL, forceRerun = FALSE)
# Get degree stats and central verteces in the TF-peak-gene graph
TF_peak_gene.degree.stats = .getDegreeStats(GRN, TF_peak_gene.df)
if (nrow(degreeDist.tbl) > 0) {
if (nrow(TF_peak_gene.df) > 0) {
#degreeDist.tbl = TF_peak_gene.degree.stats$tbl$degrees
gDegrees = TF_peak_gene.degree.stats$figures$degreeDist + ggtitle("Distribution of vertex degrees in the filtered GRN")
gTopGenes = TF_peak_gene.degree.stats$figures$topGenes + ggtitle("Top degree-central genes in the filtered GRN")
......
src/GRaNIEdev/R/zzz.R
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......@@ -7,7 +7,7 @@
"See the vignettes (type browseVignettes(\"", utils::packageName(), "\") or the help pages for how to use it for your analyses.\n",
"All project-related information and ways to contact us can be found here: https://grp-zaugg.embl-community.io/grn\n"
"All project-related information and ways to contact us can be found here: https://grp-zaugg.embl-community.io/GRaNIE\n"
)
packageStartupMessage(message)
......
src/GRaNIEdev/README.md
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......@@ -40,4 +40,4 @@ If you have questions, doubts, ideas or problems, please use the [Gitlab Issue T
### Contributions
- Originally developed by Armando Reyes-Palomares and subsequently modified by Giovanni Palla
- Christian Arnold then took over and added many improvements and extensions and converted it to a proper R package with the help of various people from the Zaugg Lab
\ No newline at end of file
- Christian Arnold then took over and added many improvements and extensions and converted it to a proper R package with the help of various people from the Zaugg Lab, particularly Rim Moussa.
\ No newline at end of file
src/GRaNIEdev/docs/404.html
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......@@ -12,8 +12,8 @@
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......@@ -65,7 +68,10 @@
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......@@ -78,7 +84,7 @@
</header><div class="row">
</header><script src="Introduction_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Introduction and Methodological Details</h1>
......@@ -94,7 +100,7 @@
<div class="abstract">
<p class="abstract">Abstract</p>
This vignette introduces the <code>GRaNIE</code> package and explains the main features, methods and necessary background.
<p>This vignette introduces the <code>GRaNIE</code> package and explains the main features, methods and necessary background.</p>
</div>
<div id="motivation" class="section level1">
......
src/GRaNIEdev/docs/articles/Introduction_files/header-attrs-2.11/header-attrs.js 0 → 100644
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
src/GRaNIEdev/docs/articles/index.html
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......@@ -12,8 +12,8 @@
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......@@ -105,7 +112,10 @@
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......@@ -127,14 +137,28 @@
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......@@ -65,7 +68,10 @@
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......@@ -78,7 +84,7 @@
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</header><script src="quickStart_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
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a = h.attributes;
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src/GRaNIEdev/docs/articles/workflow_files/header-attrs-2.11/header-attrs.js 0 → 100644
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
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......@@ -12,8 +12,8 @@
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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