Commit 48aa9266 authored by smorabit's avatar smorabit
Browse files

network vis

parent b25162e7

NAMESPACE

+10 −0
Original line number Diff line number Diff line
@@ -6,10 +6,12 @@ export(ComputeROC) 
export(ConstructMetacells)

export(ConstructNetwork)

export(DimPlotMetacells)

export(DoHubGeneHeatmap)

export(EnrichrBarPlot)

export(EnrichrDotPlot)

export(GetDatExpr)

export(GetMEs)

export(GetMultiExpr)

export(HubGeneNetworkPlot)

export(MetacellsByGroups)

export(ModuleConnectivity)
@@ -19,20 +21,28 @@ export(ModuleEigengenes) 
export(ModuleExprScore)

export(ModuleFeaturePlot)

export(ModuleNetworkPlot)

export(ModuleTraitCorrelation)

export(ModuleUMAPPlot)

export(MotifOverlapBarPlot)

export(MotifScan)

export(MotifTargetScore)

export(NormalizeMetacells)

export(OverlapBarPlot)

export(OverlapDotPlot)

export(OverlapModulesDEGs)

export(OverlapModulesMotifs)

export(PlotDendrogram)

export(ProjectModules)

export(ROCCurves)

export(RunEnrichr)

export(RunHarmonyMetacells)

export(RunModuleUMAP)

export(RunPCAMetacells)

export(RunUMAPMetacells)

export(ScaleMetacells)

export(SelectNetworkGenes)

export(SetDatExpr)

export(SetMultiExpr)

export(SetupForWGCNA)

export(TestSoftPowers)

export(TransferModuleGenome)

R/plotting.R

+79 −55
Original line number Diff line number Diff line
@@ -419,7 +419,7 @@ ModuleFeaturePlot<- function( 
#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -515,7 +515,7 @@ EnrichrBarPlot <- function( 
#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -586,10 +586,11 @@ EnrichrDotPlot <- function( 




  p <- plot_df  %>%

    ggplot(aes(x=module, y=rev(Term))) +

    ggplot(aes(x=module, y=Term)) +

    geom_point(aes(size=Combined.Score), color=plot_df$color) +

    RotatedAxis() +

    ylab('') + xlab('') + labs(size=lab) +

    scale_y_discrete(limits=rev) +

    ggtitle(database) +

    theme(

      plot.title = element_text(hjust = 0.5),
@@ -604,21 +605,27 @@ EnrichrDotPlot <- function( 


#' ModuleNetworkPlot

#'

#' Makes barplots from Enrichr data

#' Visualizes the top hub genes for selected modules as a circular network plot

#'

#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param mods Names of the modules to plot. If mods = "all", all modules are plotted.

#' @param outdir The directory where the plots will be stored.

#' @param plot_size A vector containing the width and height of the network plots.

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

#' ModuleNetworkPlot

ModuleNetworkPlot <- function(

  seurat_obj, mods="all", outdir="ModuleNetworks",

  plot_size = c(6,6), wgcna_name=NULL,

  seurat_obj,

  mods="all",

  outdir="ModuleNetworks",

  plot_size = c(6,6),

  wgcna_name=NULL,

  label_center = FALSE, # only label the genes in the middle?

  edge.alpha=0.25, vertex.label.cex=1, vertex.size=6, ...

  edge.alpha=0.25,

  vertex.label.cex=1,

  vertex.size=6, ...

){



  # get data from active assay if wgcna_name is not given
@@ -726,21 +733,35 @@ ModuleNetworkPlot <- function( 


#' HubGeneNetworkPlot

#'

#' Makes barplots from Enrichr data

#' Construct a unified network plot comprising hub genes for multiple modules.

#'

#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param mods Names of the modules to plot. If mods = "all", all modules are plotted.

#' @param n_hubs The number of hub genes to plot for each module.

#' @param n_other The number of non-hub genes to sample from each module

#' @param edge_prop The proportion of edges in the graph to sample.

#' @param return_graph logical determining whether we return the graph (TRUE) or plot the graph (FALSE)

#' @param edge.alpha Scaling factor for the edge opacity

#' @param vertex.label.cex The font size of the gene labels

#' @param hub.vertex.size The size of the hub gene nodes

#' @param other.vertex.size The size of the other gene nodes

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

#' HubGeneNetworkPlot

HubGeneNetworkPlot <- function(

  seurat_obj, mods="all", n_hubs=6, n_other=3,

  plot_size = c(6,6), wgcna_name=NULL,

  edge.alpha=0.25, vertex.label.cex=0.5, hub.vertex.size=4,

  other.vertex.size=1, repulse.exp=3,  ...

  seurat_obj, mods="all",

  n_hubs=6, n_other=3,

  sample_edges = TRUE,

  edge_prop = 0.5,

  return_graph=FALSE,

  edge.alpha=0.25,

  vertex.label.cex=0.5,

  hub.vertex.size=4,

  other.vertex.size=1,

  wgcna_name=NULL,

  ...

){



  # get data from active assay if wgcna_name is not given
@@ -789,21 +810,13 @@ HubGeneNetworkPlot <- function( 
  selected_modules$label <- ifelse(selected_modules$geneset == 'hub', as.character(selected_modules$gene_name), '')

  selected_modules$fontcolor <- ifelse(selected_modules$color == 'black', 'gray50', 'black')



  print(table(selected_modules$module))



  # make sure all nodes have at least one edge!!

  edge_cutoff <- min(sapply(1:nrow(subset_TOM), function(i){max(subset_TOM[i,])}))

  edge_df <- subset_TOM %>% melt %>% subset(value >= edge_cutoff)



  # remove nodes with fewer than n edges:

  n_fewer = 5

  remove_nodes <- table(edge_df$Var1)[table(edge_df$Var1) < n_fewer] %>% names

  edge_df <- subset(edge_df, !(Var1 %in% remove_nodes) & !(Var2 %in% remove_nodes))

  selected_modules <- subset(selected_modules, !(gene_name %in% remove_nodes))

  edge_df <- reshape2::melt(subset_TOM) %>% subset(value >= edge_cutoff)



  # scale edge values between 0 and 1

  edge_df$value <- scale01(edge_df$value)



  # set color of each edge based on value:

  edge_df$color <- sapply(1:nrow(edge_df), function(i){

  edge_df$color <- future.apply::future_sapply(1:nrow(edge_df), function(i){

    gene1 = as.character(edge_df[i,'Var1'])

    gene2 = as.character(edge_df[i,'Var2'])
@@ -818,6 +831,34 @@ HubGeneNetworkPlot <- function( 
    col

  })



  # subset edges:

  groups <- unique(edge_df$color)

  print(groups)

  if(sample_edges){

    print('here')

    # randomly sample

    temp <- do.call(rbind, lapply(groups, function(cur_group){

      cur_df <- edge_df %>% subset(color == cur_group)

      n_edges <- nrow(cur_df)

      cur_sample <- sample(1:n_edges, round(n_edges * edge_prop))

      cur_df[cur_sample,]

    }))

  } else{



    # get top strongest edges

    temp <- do.call(rbind, lapply(groups, function(cur_group){

      cur_df <- edge_df %>% subset(color == cur_group)

      n_edges <- nrow(cur_df)

      cur_df %>% dplyr::top_n(round(n_edges * edge_prop), wt=value)

    }))

  }



  edge_df <- temp

  print(dim(edge_df))



  # scale edge values between 0 and 1 for each module

  edge_df <- edge_df %>% group_by(color) %>% mutate(value=scale01(value))



  edge_df$color <- sapply(1:nrow(edge_df), function(i){

    a = edge_df$value[i]

    #if(edge_df$value[i] < 0.05){a=0.05}
@@ -830,25 +871,9 @@ HubGeneNetworkPlot <- function( 
    vertices=selected_modules

  )



  # qgraph layout

  e <-  get.edgelist(g, name=FALSE)

  l <- qgraph.layout.fruchtermanreingold(

    e, vcount = vcount(g),

    weights=edge_df$value,

    repulse.rad=(vcount(g)^repulse.exp),

    #cool.exp = 0.5,

    niter=2500,

    #max.delta = vcount(g)/2

  )



  # make a communities? (nope, this looks bad)

  # comm <- igraph::make_clusters(

  #   g,

  #   membership=as.numeric(as.factor(V(g)$module)),

  #   algorithm="scWGCNA"

  # )

  l <- igraph::layout_with_fr(g, ...)



  # label vertices?

  if(return_graph){return(g)}



  plot(

    g, layout=l,
@@ -892,7 +917,6 @@ ModuleUMAPPlot <- function( 
  vertex.label.cex=0.5,

  hub.vertex.size=4,

  other.vertex.size=1,

  repulse.exp=3,

    return_graph = FALSE, # this returns the igraph object instead of plotting

  wgcna_name=NULL,

  ...
@@ -1039,7 +1063,7 @@ ModuleUMAPPlot <- function( 
#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -1087,7 +1111,7 @@ OverlapDotPlot <- function( 
#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -1156,7 +1180,7 @@ OverlapBarPlot <- function( 
#' @param seurat_obj A Seurat object

#' @param dbs List of EnrichR databases

#' @param max_genes Max number of genes to include per module, ranked by kME.

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -1227,7 +1251,7 @@ ROCCurves <- function( 
#' Displays the top n TFs in a set of modules as a bar plot

#'

#' @param seurat_obj A Seurat object

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples
@@ -1332,7 +1356,7 @@ MotifOverlapBarPlot <- function( 
#'

#'

#' @param seurat_obj A Seurat object

#' @param wgcna_name

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

_pkgdown.yml

+2 −2
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ authors: 
navbar:

 components:

   articles:

    text: Articles

    text: Vignettes

    menu:

    - text: Core functionality

    - text: scWGCNA basics
@@ -37,7 +37,7 @@ navbar: 
    - text: Projecting modules onto new datasets

      href: articles/projecting_modules.html

    - text: -------

    - text: All articles

    - text: All vignettes

      href: articles/index.html

docs/404.html

+3 −3
Original line number Diff line number Diff line
@@ -44,8 +44,8 @@ 
  <a class="nav-link" href="https://smorabit.github.io/scWGCNA/reference/index.html">Reference</a>

</li>

<li class="nav-item dropdown">

  <a href="https://smorabit.github.io/scWGCNA/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-articles">

  <a href="https://smorabit.github.io/scWGCNA/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-vignettes">Vignettes</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-vignettes">

    <h6 class="dropdown-header" data-toc-skip>Core functionality</h6>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/basic_tutorial.html">scWGCNA basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/network_visualizations.html">Network visualization</a>
@@ -59,7 +59,7 @@ 
    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/motif_analysis.html">Motif analysis</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/projecting_modules.html">Projecting modules onto new datasets</a>

    <div class="dropdown-divider"></div>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/index.html">All articles</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/index.html">All vignettes</a>

  </div>

</li>

      </ul>

docs/LICENSE-text.html

+3 −3
Original line number Diff line number Diff line
@@ -22,8 +22,8 @@ 
  <a class="nav-link" href="reference/index.html">Reference</a>

</li>

<li class="nav-item dropdown">

  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-articles">

  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-vignettes">Vignettes</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-vignettes">

    <h6 class="dropdown-header" data-toc-skip>Core functionality</h6>

    <a class="dropdown-item" href="articles/basic_tutorial.html">scWGCNA basics</a>

    <a class="dropdown-item" href="articles/network_visualizations.html">Network visualization</a>
@@ -37,7 +37,7 @@ 
    <a class="dropdown-item" href="articles/motif_analysis.html">Motif analysis</a>

    <a class="dropdown-item" href="articles/projecting_modules.html">Projecting modules onto new datasets</a>

    <div class="dropdown-divider"></div>

    <a class="dropdown-item" href="articles/index.html">All articles</a>

    <a class="dropdown-item" href="articles/index.html">All vignettes</a>

  </div>

</li>

      </ul><form class="form-inline my-2 my-lg-0" role="search">

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