Commit 6c8325d7 authored by Christian Arnold's avatar Christian Arnold
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Documentatio updates, fixes an issue with the AR summary heatmap to produce an...

Documentatio updates, fixes an issue with the AR summary heatmap to produce an empty PDF due to a bug in pheatmap
parent 5b366a6b
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^.*\.Rproj$
^\.Rproj\.user$
^doc$
^Meta$
^_pkgdown\.yml$
^docs$
^pkgdown$
pkgdown/
Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.14.5
Version: 0.14.6
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
......
......@@ -4404,6 +4404,8 @@ calculateGeneralEnrichment <- function(GRN, ontology = c("BP", "MF"),
GRN
}
# TODO: Put TF.ensebl and not TF.name to avoid redundancy
.generateGraphTables <- function(GRN){
# This function returns the tf-peak-gene and the tf-gene graphs in dataframe format
......
......@@ -742,10 +742,18 @@
}
labelMain = paste0(as.numeric(thresCur)*100, " / ", (1 - as.numeric(thresCur))*100, " %")
labelMain = "Summary density heatmap for each TF\nand classifications across stringencies"
pheatmap::pheatmap(diffDensityMat_Plot, cluster_rows = FALSE, cluster_cols = FALSE,
fontsize_row = 1.25, scale = 'row' , fontsize_col = 10, fontsize = 8, labels_col = c(-1, -0.5, 0, 0.5, 1),
annotation_row = anno_rowDF, annotation_colors = annotation_colors, annotation_legend = FALSE, main = labelMain, legend = TRUE)
labelMain = "Summary density heatmap (foreground - background)\nfor each TF and classifications across stringencies"
# pheatmap::pheatmap(diffDensityMat_Plot, cluster_rows = FALSE, cluster_cols = FALSE,
# fontsize_row = 1.25, scale = 'row' , fontsize_col = 10, fontsize = 8, labels_col = c(-1, -0.5, 0, 0.5, 1),
# annotation_row = anno_rowDF, annotation_colors = annotation_colors, annotation_legend = FALSE, main = labelMain, legend = TRUE)
# Run a modified version here, see function documentation for details
p = .pheatmap_mod(diffDensityMat_Plot, cluster_rows = FALSE, cluster_cols = FALSE,
fontsize_row = 1.25, scale = 'row' , fontsize_col = 10, fontsize = 8, labels_col = c(-1, -0.5, 0, 0.5, 1),
annotation_row = anno_rowDF, annotation_colors = annotation_colors, annotation_legend = FALSE, main = labelMain, legend = TRUE, silent = TRUE)
grid::grid.newpage()
grid::grid.draw(p$gtable)
if (!is.null(file)) {
......
......@@ -418,7 +418,7 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), top
# Preprocess matrix
mat = as.matrix(mat)
if(scale != "none"){
mat = scale_mat(mat, scale)
mat = pheatmap:::scale_mat(mat, scale)
if(pheatmap:::is.na2(breaks)){
breaks = pheatmap:::generate_breaks(mat, length(color), center = TRUE)
}
......@@ -428,7 +428,7 @@ plotPCA_all <- function (GRN, outputFolder = NULL, type = c("rna", "peaks"), top
# Kmeans
if(!is.na(kmeans_k)){
# Cluster data
km = stats:.kmeans(mat, kmeans_k, iter.max = 100)
km = stats::kmeans(mat, kmeans_k, iter.max = 100)
mat = km$centers
# Compose rownames
......@@ -662,7 +662,7 @@ plotDiagnosticPlots_TFPeaks <- function(GRN,
fileCur = paste0(outputFolder, .getOutputFileName("plot_TFPeak_fdr"), suffixFile)
if (!file.exists(fileCur) | forceRerun) {
heightCur = 4* length(GRN@config$TF_peak_connectionTypes)
heightCur = 8* length(GRN@config$TF_peak_connectionTypes)
.plot_TF_peak_fdr(GRN, perm = permutationCur, useGCCorrection = useGCCorrection, plotDetails = plotDetails, fileCur, width = 7, height = heightCur)
}
......
development:
mode: unreleased
url: https://grp-zaugg.embl-community.io/GRaNIE
template:
params:
bootswatch: flatly
ganalytics: G-530L9SXFM1
news:
one_page: false
includes:
in_header: |
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gtag('js', new Date());
gtag('config', 'G-YZH9WY9PBP');
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navbar:
left:
......@@ -46,51 +59,3 @@ articles:
navbar: Workflow Vignette
contents:
- workflow
#
# navbar:
# left:
# - href: index.html
# - text: Getting Started
# href: articles/GRaNIE.html
# - text: Vignettes
# menu:
# - text: Getting started
# desc: Bla
# href: articles/GRaNIE.html
# navbar: Test
# - text: Introduction
# desc: Learn what the GRaNIE package is and what you can use it for
# navbar: Intro
# href: articles/Introduction.html
# - text: Workflow example
# desc: Learn how to use the GRaNIE package with a full workflow example
# href: articles/workflow.html
# navbar: test
# - text: Reference
# href: reference/index.html
# - text: Changelog & News
# href: news/index.html
#
# navbar:
# left:
# - href: index.html
# - text: Getting Started
# href: articles/GRaNIE.html
# - text: Vignettes
# menu:
# - text: Plot Assembly
# href: articles/guides/assembly.html
# - text: Controlling Layout
# href: articles/guides/layout.html
# - text: Adding annotation to a patchwork
# href: articles/guides/annotation.html
# - text: Multipage Alignment
# href: articles/guides/multipage.html
# - text: Reference
# href: reference/index.html
# - text: News
#
# See https://github.com/thomasp85/patchwork/blob/master/_pkgdown.yml for a full customized example
......@@ -6,27 +6,32 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Page not found (404) • GRaNIE</title>
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......@@ -43,42 +48,42 @@
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.5</span>
<a class="navbar-link" href="https://grp-zaugg.embl-community.io/GRaNIE/index.html">GRaNIE</a>
<span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="Unreleased version">0.14.6</span>
</span>
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