working on module projection tutorials (515eb42d) · Commits · github_fork / HdWGCNA

DESCRIPTION

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		@@ -3,7 +3,8 @@ Title: WGCNA
		Version: 0.0.0.9000
		Authors@R: c(
		person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0002-7768-4856"))
		comment = c(ORCID = "0000-0002-7768-4856")),
		person("Swarup Lab", role = "fnd")
		)
		Description: scWGCNA is an R package for performing weighted gene co-expression network analysis in single-cell RNA-seq data.
		License: MIT + file LICENSE

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		@@ -1544,7 +1544,7 @@ DoHubGeneHeatmap <- function(
		PlotModulePreservation <- function(
		seurat_obj,
		name,
		statistics = 'summary', # can be summary, all, or a custom list
		statistics = 'summary', # can be summary, rank, all, or a custom list
		plot_labels = TRUE,
		label_size = 4,
		mod_point_size = 4,
		@@ -1567,7 +1567,9 @@ PlotModulePreservation <- function(

		# what are we going to plot?
		if(statistics == 'summary'){
		stat_list <- c("medianRank.pres", "Zsummary.pres")
		stat_list <- c("Zsummary.qual", "Zsummary.pres")
		} else if(statistics == 'rank'){
		stat_list <- colnames(obs_df[,-1])[grepl("Rank", colnames(obs_df[,-1]))]
		} else if(statistics == 'all'){
		stat_list <- c(colnames(obs_df[,-1])[grepl("Rank", colnames(obs_df[,-1]))], colnames(Z_df[,-1]))
		} else{
		@@ -1576,7 +1578,6 @@ PlotModulePreservation <- function(

		stat_list <- stat_list[stat_list != 'moduleSize']


		plot_list <- list()
		for(statistic in stat_list){

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		@@ -14,6 +14,8 @@ home:
		authors:
		Sam Morabito:
		href: https://smorabit.github.io
		Swarup Lab:
		href: https://swaruplab.bio.uci.edu/

		navbar:
		structure:

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		@@ -143,7 +143,7 @@ Content not found. Please use links in the navbar.

		<footer><div class="copyright">
		<p></p>
		<p>Developed by <a href="https://smorabit.github.io" class="external-link">Sam Morabito</a>.</p>
		<p>Developed by <a href="https://smorabit.github.io" class="external-link">Sam Morabito</a>, <a href="https://swaruplab.bio.uci.edu/" class="external-link">Swarup Lab</a>.</p>
		</div>

		<div class="pkgdown">

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		@@ -112,7 +112,7 @@


		<footer><div class="copyright">
		<p></p><p>Developed by <a href="https://smorabit.github.io" class="external-link">Sam Morabito</a>.</p>
		<p></p><p>Developed by <a href="https://smorabit.github.io" class="external-link">Sam Morabito</a>, <a href="https://swaruplab.bio.uci.edu/" class="external-link">Swarup Lab</a>.</p>
		</div>

		<div class="pkgdown">