R/viz.R
In BlishLab/scriabin: Single-cell resolved interaction analysis through binning
Defines functions
PearsonDist
PlotAlluviumLT
IPFeaturePlot
CCIMFeaturePlot
PlotAlluvium_nocells
BuildGranHeatmap
BuildSingleHeatmap
PlotAlluvium
PrioritizeInteractome
PlotAlluviumLigRec
HighlightSR
BuildCompHeatmap
BuildVarianceHeatmap
BuildRVHeatmap
Documented in
BuildCompHeatmap
BuildGranHeatmap
BuildRVHeatmap
BuildSingleHeatmap
BuildVarianceHeatmap
CCIMFeaturePlot
HighlightSR
IPFeaturePlot
PearsonDist
PlotAlluvium
PlotAlluviumLigRec
PlotAlluviumLT
PlotAlluvium_nocells
PrioritizeInteractome
#' Title
#'
#' @param interaction_graphs
#' @param name
#'
#' @return
#' @export
#'
#' @examples
BuildRVHeatmap <- function(interaction_graphs, name = "rv_results") {
interaction_graphs <- lapply(interaction_graphs, function(x) {x[[1]]})
ig_ktab <- ktab.list.df(lapply(interaction_graphs,as.data.frame))
rv_results <- statis(ig_ktab, scannf=F)
mat_plot <- rv_results$RV
colnames(mat_plot) <- translateTimes(colnames(mat_plot))
rownames(mat_plot) <- translateTimes(rownames(mat_plot))
max_value = quantile(mat_plot,0.99, na.rm=T)
mid_value = quantile(mat_plot,0.75, na.rm=T)
min_value = quantile(mat_plot,0.01, na.rm=T)
col_fun.use = colorRamp2(c(min_value,mid_value,max_value), c("#08306B","grey80","white"))
# col_fun.use = colorRamp2(breaks = c(min_value,mid_value,2), colors = c("yellow","purple","black"))
# pdf(paste0("~/Downloads/",name,".pdf"), height = 5, width = 7)
Heatmap(mat_plot, cluster_rows = F, cluster_columns = F, name = "RV\ncoef", col = col_fun.use)
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
BuildVarianceHeatmap <- function(interaction_graphs, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2",
cell.cols = NULL) {
resample <- function(x, ...) x[sample.int(length(x), ...)]
f1 <- function(lst) {
n <- length(lst)
rc <- dim(lst[[1]])
ar1 <- array(unlist(lst), c(rc, n))
var_results <- apply(ar1, c(1, 2), sd)
median_results <- apply(ar1, c(1, 2), median)
median_results <- rep(median_results,n)
time_results <- abs(ar1-median_results)
# pre_results <- rep(lst[[1]],n)
# time_results <- abs(ar1-pre_results)
time_results <- apply(time_results,c(1, 2), function(y) {resample(which(y==max(y)),1)})
time_results <- mapvalues(time_results, from = 1:n, to = names(lst))
return(list(var_results,time_results))
}
results <- f1(interaction_graphs)
var_results <- results[[1]]
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
time_results <- results[[2]]
rownames(time_results) <- rownames(interaction_graphs[[1]])
colnames(time_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
if(is.null(cell.cols)) {
cell.cols <- pal_igv()(length(unique(nbct.f$celltype)))
names(cell.cols) <- unique(nbct.f$celltype)
}
cell.cols_use <- cell.cols[names(cell.cols) %in% nbct.f$celltype]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1)),
show_legend = c(T,F))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1),
"SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,F))
}
#
max_value = quantile(var_results,0.99)
col_fun.use = colorRamp2(c(0,max_value), c("white","#08306B"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
# time_results <- translateTimes(time_results)
hc = hclust(dist(t(var_results), method="euclidean"), method = "complete")
hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
cluster_columns = hc, column_dend_reorder = F,
name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
thm <- Heatmap(time_results, name = "Timepoint",
# col = time.cols,
cluster_columns = hc, column_dend_reorder = F, show_column_dend = T,
show_row_names = F, show_column_names = F)
return(list(SCluster=row_grp,RCluster=col_grp,var_hm=hm,time_hm=thm))
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param ident.1
#' @param ident.2
#' @param row.k
#' @param col.k
#'
#' @return
#' @export
#'
#' @examples
BuildCompHeatmap <- function(interaction_graphs, seu, name = "var_results", ident.1 = NULL, ident.2 = "pre",
row.k = NULL, col.k = NULL) {
var_results <- abs(interaction_graphs[[ident.1]]-interaction_graphs[[ident.2]])
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu$celltype.l2,seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
cell.cols <- pal_igv()(length(unique(nbct.f$celltype)))
names(cell.cols) <- unique(nbct.f$celltype)
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols,
"SCluster" = row.colors))
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols,
"RCluster" = col.colors),
annotation_name_side = "left")
# pdf(paste0("~/Downloads/",name,".pdf"), height = 7, width = 9.5)
p <- Heatmap(var_results, show_row_names = T, show_column_names = T,
name = "Diff", top_annotation = ta, left_annotation = la,
row_names_gp = gpar(fontsize=0), column_names_gp = gpar(fontsize=0))
return(list(SCluster=row_grp,RCluster=col_grp,Heatmap=p))
}
#' Title
#'
#' @param seu
#' @param interactome
#' @param subset.time
#'
#' @return
#' @export
#'
#' @examples
HighlightSR <- function(seu, interactome, subset.time = NULL) {
if(!is.null(subset.time)) {
seu <- subset(seu, cells = colnames(seu)[seu$time.orig==subset.time])
message("Running PCA")
seu <- RunPCA(seu, verbose = F)
message("Running UMAP")
seu <- RunUMAP(seu, dims = 1:50, verbose = F)
}
cells = list(Senders = unique(interactome$source),
Receivers = unique(interactome$receiver))
DimPlot(seu, cells.highlight = cells, cols.highlight = list("blue","red")) + NoLegend() + theme_umap() +
labs(x = "UMAP1", y = "UMAP2")
}
#' Title
#'
#' @param connectome
#'
#' @return
#' @export
#'
#' @examples
PlotAlluviumLigRec <- function(connectome) {
connectome_plot <- connectome[,c("source_type","source","ligand","receptor","target","target_type","weight")]
colnames(connectome_plot) <- c("Sender\ncelltype","Sender\ncell","Ligand",
"Receptor","Receiver\ncell","Receiver\ncelltype","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:6, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum, fill = Weight)) +
geom_flow(stat = "alluvium", lode.guidance = "frontback",
color = "darkgray") +
geom_stratum() +
ggrepel::geom_text_repel(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6), as.character(stratum), NA)),
stat = "stratum", size = 4, direction = "y") +
theme_cowplot() + scale_fill_gradient(low = "grey50", high = "red") +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL)
}
#' Title
#'
#' @param seu
#' @param gene_rankings
#' @param interactome
#' @param min.pct
#' @param assay.use
#' @param slot.use
#' @param send_cells
#' @param rec_cells
#'
#' @return
#' @export
#'
#' @examples
PrioritizeInteractome <- function(seu, gene_rankings, interactome,
min.pct = 0.05, assay.use = "RNA", slot.use = "counts",
send_cells = NULL, rec_cells = NULL) {
if(is.null(send_cells)) {
send_cells = unique(interactome$source)
}
if(is.null(rec_cells)) {
rec_cells = unique(interactome$receiver)
}
s.exprs <- GetAssayData(seu, assay = assay.use, slot = slot.use)[,send_cells]
r.exprs <- GetAssayData(seu, assay = assay.use, slot = slot.use)[,rec_cells]
s.expressed_genes <- rownames(s.exprs)[(Matrix::rowSums(s.exprs !=0)/ncol(s.exprs))>min.pct]
r.expressed_genes <- rownames(r.exprs)[(Matrix::rowSums(r.exprs !=0)/ncol(r.exprs))>min.pct]
background_expressed_genes <- r.expressed_genes %>% .[. %in% rownames(ligand_target_matrix)]
ligands = lr_network %>% pull(from) %>% unique()
receptors = lr_network %>% pull(to) %>% unique()
expressed_ligands = intersect(ligands,s.expressed_genes)
expressed_receptors = intersect(receptors,r.expressed_genes)
potential_ligands = lr_network %>% dplyr::filter(from %in% expressed_ligands & to %in% expressed_receptors) %>% pull(from) %>% unique()
gene_rankings = gene_rankings[names(gene_rankings) %in% rec_cells]
message("Beginning NicheNet")
nichenet.results <- pblapply(gene_rankings, function(x) {
activities <- predict_ligand_activities(geneset = names(x),
ligand_target_matrix = ligand_target_matrix,
potential_ligands = potential_ligands,
background_expressed_genes = background_expressed_genes)
best_upstream_ligands = activities %>%
top_n(20, pearson) %>%
arrange(-pearson) %>%
pull(test_ligand) %>%
unique()
active_ligand_target_links_df = best_upstream_ligands %>%
lapply(get_weighted_ligand_target_links,
geneset = names(x),
ligand_target_matrix = ligand_target_matrix, n = 200) %>%
bind_rows %>% drop_na()
return(list(activities,active_ligand_target_links_df))
})
return(nichenet.results)
}
#' Title
#'
#' @param connectome
#' @param optimize.flows
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
PlotAlluvium <- function(connectome, optimize.flows = T, cell.cols = NULL) {
# if(nrow(connectome)>1e5) {
# connectome <- connectome %>% group_by(source,receiver,pair) %>% top_n(n=10,wt=target_weight)
# }
connectome_plot <- as.data.frame(connectome[,c("source_type","source","ligand","receptor","receiver","receiver_type","target","edgeweight")])
colnames(connectome_plot) <- c("Sender\ncelltype","Sender\ncell","Ligand",
"Receptor","Receiver\ncell","Receiver\ncelltype","Target\ngene","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:7, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
#to distinguish senders from receivers, so coloring doesn't fail in case the same cell is in each (we want to treat them separately)
connectome_lodes$stratum <- apply(connectome_lodes,1,function(x) {
x[4] <- ifelse(x[3]=="Sender\ncell",paste0(x[4],"_send"),x[4])
})
if(is.null(cell.cols)) {
ct <- unique(c(connectome$source_type,connectome$receiver_type))
cell.cols <- pal_igv()(length(ct))
names(cell.cols) <- ct
}
sender_fill <- cell.cols
unique_genes <- unique(c(connectome_plot$Ligand,
connectome_plot$Receptor,
connectome_plot$`Target
gene`))
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
cells <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Receiver\ncell","Sender\ncell"),"stratum"]))
senders <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Sender\ncell"),"stratum"]))
receivers <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Receiver\ncell"),"stratum"]))
senders_weights <- aggregate(connectome_lodes[connectome_lodes$stratum %in% senders,"Weight"],by = list(connectome_lodes[connectome_lodes$stratum %in% senders,"stratum"]), sum) %>% arrange(x)
senders_fill <- colorRampPalette(c("grey80","yellow","red"))(nrow(senders_weights))
names(senders_fill) <- senders_weights$Group.1
receivers_weights <- aggregate(connectome_lodes[connectome_lodes$stratum %in% receivers,"Weight"],by = list(connectome_lodes[connectome_lodes$stratum %in% receivers,"stratum"]), sum) %>% arrange(x)
receivers_fill <- colorRampPalette(c("grey80","yellow","red"))(nrow(receivers_weights))
names(receivers_fill) <- receivers_weights$Group.1
cell_fill <- c(receivers_fill,senders_fill)
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
##attempt to make all cells equal. But I'm not sure you can (easily) or should.
##Because it's not an even mix and match between senders and receivers.
##You can scale all the senders to be the same, but that doesn't guarantee that the all the receivers will be the same, or vice versa.
# if(cells.equal){
# #calculate number of lodes per cell
# connectome_cells <- connectome_lodes[connectome_lodes$stratum %in% cells,]
# connectome_cells$stratum <- as.character(connectome_cells$stratum)
# lpc <- as.data.frame(table(connectome_cells$stratum))
# lpc$Freq <- (1/lpc$Freq)
# wpc <- unique(connectome_cells)[,c("Cohort","stratum")]
# wpc$Weight <- mapvalues(wpc$stratum, from = lpc$Var1, to = lpc$Freq)
# connectome_lodes$Weight <- mapvalues(connectome_lodes$Cohort, from = wpc$Cohort, to = wpc$Weight)
# }
# connectome_lodes$Weight <- 1
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
send_to_cell <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncelltype",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Sender\ncell",c("Cohort","x","stratum")],
by = "Cohort")
send_to_cell$stratum.x <- paste(send_to_cell$stratum.x,"send",sep = "_")
cell_to_ligand <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncell",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
by = "Cohort")
cell_to_ligand$stratum.y <- paste(cell_to_ligand$stratum.y,"ligand", sep = "_")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"receptor", sep = "_")
receptor_to_receiver <- merge(connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receiver\ncell",c("Cohort","x","stratum")],
by = "Cohort")
receptor_to_receiver$stratum.x <- paste(receptor_to_receiver$stratum.x,"receptor", sep = "_")
receiver_to_type <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncell",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
by = "Cohort")
receiver_to_type$stratum.y <- paste(receiver_to_type$stratum.y,"receiver", sep = "_")
type_to_target <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Target\ngene",c("Cohort","x","stratum")],
by = "Cohort")
type_to_target$stratum.x <- paste(type_to_target$stratum.x,"receiver", sep = "_")
type_to_target$stratum.y <- paste(type_to_target$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=send_to_cell$stratum.x,target=send_to_cell$stratum.y,value=1),
data.frame(source=cell_to_ligand$stratum.x,target=cell_to_ligand$stratum.y,value=1),
data.frame(source=ligand_to_receptor$stratum.x,target=ligand_to_receptor$stratum.y,value=1),
data.frame(source=receptor_to_receiver$stratum.x,target=receptor_to_receiver$stratum.y,value=1),
data.frame(source=receiver_to_type$stratum.x,target=receiver_to_type$stratum.y,value=1),
data.frame(source=type_to_target$stratum.x,target=type_to_target$stratum.y,value=1))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-2),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Sender\ncelltype",
paste(connectome_lodes_merge$stratum,"send",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receptor",
paste(connectome_lodes_merge$stratum,"receptor",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receiver\ncelltype",
paste(connectome_lodes_merge$stratum,"receiver",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target\ngene",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
send_fill <- sender_fill
names(send_fill) <- paste(names(send_fill),"send", sep = "_")
receiver_fill <- sender_fill
names(receiver_fill) <- paste(names(receiver_fill),"receiver", sep = "_")
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
receptor_fill <- gene_fill
names(receptor_fill) <- paste(names(receptor_fill),"receptor", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(send_fill,
receiver_fill,
ligand_fill,
receptor_fill,
target_fill,
cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(sender_fill,gene_fill,cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Title
#'
#' @param interaction_graph
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
BuildSingleHeatmap <- function(interaction_graph, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2",
cell.cols = NULL) {
interaction_graph <- as.matrix(interaction_graph)
#cluster rows
message("Clustering rows")
input = interaction_graph
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward.D")
if(!is.null(row.k)) {
nclust = row.k
}
else {
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(interaction_graph)
message("Clustering columns")
#cluster columns
input = t(interaction_graph)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward.D")
if(!is.null(col.k)) {
nclust = col.k
}
else {
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(interaction_graph)
# nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
# colnames(nbct) <- c("celltype","nb","freq")
# nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
message("Building annotation")
nbct.f <- data.frame(nb=colnames(seu),celltype=seu@meta.data[,cell.type.calls]) %>%
dplyr::filter(nb %in% rownames(interaction_graph))
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(interaction_graph),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(interaction_graph),as.character(nbct.f$nb)),]
if(is.null(cell.cols)) {
cell.cols <- pal_igv()(length(unique(seu@meta.data[,cell.type.calls])))
names(cell.cols) <- unique(seu@meta.data[,cell.type.calls])
}
cell.cols_use <- cell.cols[names(cell.cols) %in% nbct.f$celltype]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("SCluster" = row_grp,
col = list("SCluster" = row.colors),
show_legend = c(F))
ta = columnAnnotation("RCluster" = col_grp,
col = list("RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("SCluster" = row_grp,
col = list("SCluster" = row.colors),
annotation_legend_param = list("SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("RCluster" = col_grp,
col = list("RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F))
}
#
max_value = quantile(interaction_graph,0.99)
col_fun.use = colorRamp2(c(0,max_value), c("white","#08306B"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(interaction_graph, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
message("Building Heatmap")
hm <- Heatmap(interaction_graph, show_row_names = F, show_column_names = F,
name = "Interaction\nscore", top_annotation = ta, left_annotation = la, col = col_fun.use,
row_split = rowanno$celltype, column_split = colanno$celltype,
clustering_distance_rows = "euclidean", clustering_method_rows = "ward.D",
clustering_distance_columns = "euclidean", clustering_method_columns = "ward.D")
return(list(SCluster=row_grp,RCluster=col_grp,hm=hm))
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#'
#' @return
#' @export
#'
#' @examples
BuildGranHeatmap <- function(interaction_graphs, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2") {
resample <- function(x, ...) x[sample.int(length(x), ...)]
ig_rr <- interaction_graphs[6:9]
ig_ll <- interaction_graphs[1:5]
n <- length(ig_rr)
rc <- dim(ig_rr[[1]])
ar_rr <- array(unlist(ig_rr), c(rc, n))
n <- length(ig_ll)
rc <- dim(ig_ll[[1]])
ar_ll <- array(unlist(ig_ll), c(rc, n))
rr_mean <- apply(ar_rr, c(1, 2), mean)
ll_mean <- apply(ar_ll, c(1, 2), mean)
num <- rr_mean-ll_mean
rr_sd <- apply(ar_rr, c(1, 2), sd)
ll_sd <- apply(ar_ll, c(1, 2), sd)
rr_sd <- (rr_sd^2)/4
ll_sd <- (ll_sd^2)/5
denom <- sqrt(rr_sd+ll_sd)
var_results <- num/denom
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
row.colors <- pal_d3()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_d3()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
rowanno$celltype <- factor(as.character(rowanno$celltype),
levels = unique(c(as.character(rowanno$celltype),
as.character(colanno$celltype))))
colanno$celltype <- factor(as.character(colanno$celltype),
levels = unique(c(as.character(rowanno$celltype),
as.character(colanno$celltype))))
cell.cols_use <- cell.cols[names(cell.cols) %in% levels(rowanno$celltype)]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1)),
show_legend = c(T,F))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1),
"SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,F))
}
#
min_value = quantile(var_results,0.01)
max_value = quantile(var_results,0.99)
col_fun.use = colorRamp2(c(min_value,0,max_value), c("indianred","white","blue"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
# time_results <- translateTimes(time_results)
hc = hclust(dist(t(var_results), method="euclidean"), method = "ward")
hc1 = hclust(dist((var_results), method="euclidean"), method = "ward")
hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
cluster_columns = hc, column_dend_reorder = F,
cluster_rows = hc1, row_dend_reorder = F,
name = "T-statistic", top_annotation = ta, left_annotation = la, col = col_fun.use)
# thm <- Heatmap(time_results,col = time.cols, name = "Timepoint",
# cluster_columns = hc, column_dend_reorder = F, show_column_dend = T,
# show_row_names = F, show_column_names = F)
return(list(SCluster=row_grp,RCluster=col_grp,var_hm=hm))
}
#' Title
#'
#' @param connectome
#' @param optimize.flows
#'
#' @return
#' @export
#'
#' @examples
PlotAlluvium_nocells <- function(connectome, optimize.flows = T) {
connectome_plot <- connectome[,c("source_type","ligand","receptor","receiver_type","target","weight")]
connectome_plot$unique <- paste(connectome_plot$source_type,
connectome_plot$ligand,
connectome_plot$receptor,
connectome_plot$receiver_type,
connectome_plot$target,
sep = "_")
connectome_plot <- aggregate(connectome_plot$weight, by = list(connectome_plot$unique), FUN = sum)
colnames(connectome_plot) <- c("unique","Weight")
connectome_plot %<>% separate(unique, into = c("source_type","ligand","receptor","receiver_type","target"), sep = "_")
colnames(connectome_plot) <- c("Sender\ncelltype","Ligand",
"Receptor","Receiver\ncelltype","Target\ngene","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:5, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
sender_fill <- cell.cols
unique_genes <- unique(c(connectome_plot$Ligand,
connectome_plot$Receptor,
connectome_plot$`Target
gene`))
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
send_to_ligand <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncelltype",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
by = "Cohort")
send_to_ligand$stratum.x <- paste(send_to_ligand$stratum.x,"send",sep = "_")
send_to_ligand$stratum.y <- paste(send_to_ligand$stratum.y,"send",sep = "_")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"receptor", sep = "_")
receptor_to_type <- merge(connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
by = "Cohort")
receptor_to_type$stratum.x <- paste(receptor_to_type$stratum.x,"receiver", sep = "_")
receptor_to_type$stratum.y <- paste(receptor_to_type$stratum.y,"receiver", sep = "_")
type_to_target <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Target\ngene",c("Cohort","x","stratum")],
by = "Cohort")
type_to_target$stratum.x <- paste(type_to_target$stratum.x,"receiver", sep = "_")
type_to_target$stratum.y <- paste(type_to_target$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=send_to_ligand$stratum.x,target=send_to_ligand$stratum.y,value=send_to_ligand$Weight),
data.frame(source=ligand_to_receptor$stratum.x,target=ligand_to_receptor$stratum.y,value=ligand_to_receptor$Weight),
data.frame(source=receptor_to_type$stratum.x,target=receptor_to_type$stratum.y,value=receptor_to_type$Weight),
data.frame(source=type_to_target$stratum.x,target=type_to_target$stratum.y,value=type_to_target$Weight))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(plyr::mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(plyr::mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-2),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Sender\ncelltype",
paste(connectome_lodes_merge$stratum,"send",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receptor",
paste(connectome_lodes_merge$stratum,"receptor",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receiver\ncelltype",
paste(connectome_lodes_merge$stratum,"receiver",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target\ngene",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
send_fill <- sender_fill
names(send_fill) <- paste(names(send_fill),"send", sep = "_")
receiver_fill <- sender_fill
names(receiver_fill) <- paste(names(receiver_fill),"receiver", sep = "_")
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
receptor_fill <- gene_fill
names(receptor_fill) <- paste(names(receptor_fill),"receptor", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(stat = "alluvium", lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
geom_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(send_fill,
receiver_fill,
ligand_fill,
receptor_fill,
target_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1:5), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(sender_fill,gene_fill,cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Title
#'
#' @param ccim
#' @param seu
#' @param features
#' @param type_plot
#' @param ...
#'
#' @return
#' @import magrittr
#' @export
#'
#' @examples
CCIMFeaturePlot <- function(ccim, seu,
features = NULL,
type_plot = c("sender","receiver"), ...) {
#find cells of interest in the original object
type_plot <- match.arg(arg = type_plot, several.ok = F)
p <- FeaturePlot(seu, features = features, combine = F)
if(length(features)>1) {
pdata <- as.data.frame(t(do.call(rbind,lapply(p,function(x) {x$data[,4]}))))
colnames(pdata) <- features
rownames(pdata) <- colnames(seu)
}
else {
pdata <- as.data.frame(x=p[[1]]$data[,4])
colnames(pdata) <- features
rownames(pdata) <- colnames(seu)
}
ccim_meta <- merge((ccim@meta.data %>% rownames_to_column("cell")),
(pdata %>% rownames_to_column(type_plot)),
by = type_plot, all.y = F)
ccim_meta <- ccim_meta[match(colnames(ccim),ccim_meta$cell),]
rownames(ccim_meta) <- NULL
ccim_meta %<>%
column_to_rownames("cell")
ccim@meta.data <- ccim_meta
FeaturePlot(ccim, features = features, ... )
}
#' Plot expression of interaction programs
#'
#' @param seu A seurat object that has interaction program expression information stored in the meta.data slot as the output of `ScoreInteractionPrograms`
#' @param ip The name of the interaction program to plot
#' @param cols Character vector of colors to use for plotting
#' @param order Logical. Order points so highest expressers are on top?
#'
#' @return
#' @import ggplot2
#' @export
#'
#' @examples
IPFeaturePlot <- function(seu, ip, cols = c("grey90","blue","orangered3"), order = T) {
seu$lig_feature <- seu[["IPligands"]]@data[ip,]
seu$rec_feature <- seu[["IPreceptors"]]@data[ip,]
# p <- FeaturePlot(seu,
# features = c(paste0("ligands_",ip),
# paste0("receptors_",ip)),
# blend = T, combine = F,
# cols = cols, order = order)
p <- FeaturePlot(seu,
features = c("lig_feature","rec_feature"),
blend = T, combine = F,
cols = cols, order = order)
p[[3]] + NoLegend() + labs(x = NULL, y = NULL, title = NULL) +
theme(aspect.ratio = 1,axis.ticks = element_blank(),
axis.text = element_blank())
}
#' Plot Alluvial of ligand-target links
#'
#' @param connectome
#' @param optimize.flows
#' @param colors
#'
#' @return
#' @export
#'
#' @examples
PlotAlluviumLT <- function(connectome, optimize.flows = T, colors = NULL) {
connectome_plot <- as.data.frame(connectome[,c("ligand","target","mean")])
colnames(connectome_plot) <- c("Ligand","Target","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:2, id = "Cohort")
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
if(is.null(colors)) {
unique_genes <- unique(connectome_lodes$stratum)
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
}
else {
gene_fill <- colors
}
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Target",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=ligand_to_receptor$stratum.x,
target=ligand_to_receptor$stratum.y,value=1))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-1),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(ligand_fill,
target_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,2), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(gene_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,2), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Plot Pearson distributions for ligand activities
#'
#' @param ligand_activities the matrix output of `RankActiveLigands`
#' @param pearson_cutoff determines where to draw a vertical line illustrating the chosen Pearson threshold cutoff (default: 0.075)
#'
#' @return Two plots of all Pearson coefficients (left) and median Pearson coefficient per cell (right)
#' @export
#'
#' @examples
PearsonDist <- function(ligand_activities, pearson_cutoff = 0.075) {
ral_df <- data.frame(x = as.vector(ligand_activities))
minx <- min(ral_df$x)
maxx <- max(ral_df$x)
p1 <- ggplot(ral_df, aes(x = x)) + geom_density(fill = "steelblue") + theme_cowplot() +
labs(x = "Pearson coefficient", y = "Density", title = "All Pearson coefficients") +
xlim(c(minx,maxx)) + geom_vline(xintercept = pearson_cutoff) +
theme(plot.title = element_text(hjust = 0.5), aspect.ratio = 1)
ral_df <- data.frame(x = as.vector(apply(ligand_activities,2,median)))
p2 <- ggplot(ral_df, aes(x = x)) + geom_density(fill = "steelblue") + theme_cowplot() +
labs(x = "Pearson coefficient", y = "Density", title = "Median Pearson coefficient\nper cell") +
xlim(c(minx,maxx)) + geom_vline(xintercept = pearson_cutoff) +
theme(plot.title = element_text(hjust = 0.5), aspect.ratio = 1)
p1|p2
}
BlishLab/scriabin documentation built on Sept. 16, 2024, 1:19 a.m.
R Package Documentation
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Defines functions PearsonDist PlotAlluviumLT IPFeaturePlot CCIMFeaturePlot PlotAlluvium_nocells BuildGranHeatmap BuildSingleHeatmap PlotAlluvium PrioritizeInteractome PlotAlluviumLigRec HighlightSR BuildCompHeatmap BuildVarianceHeatmap BuildRVHeatmap
Documented in BuildCompHeatmap BuildGranHeatmap BuildRVHeatmap BuildSingleHeatmap BuildVarianceHeatmap CCIMFeaturePlot HighlightSR IPFeaturePlot PearsonDist PlotAlluvium PlotAlluviumLigRec PlotAlluviumLT PlotAlluvium_nocells PrioritizeInteractome
#' Title
#'
#' @param interaction_graphs
#' @param name
#'
#' @return
#' @export
#'
#' @examples
BuildRVHeatmap <- function(interaction_graphs, name = "rv_results") {
interaction_graphs <- lapply(interaction_graphs, function(x) {x[[1]]})
ig_ktab <- ktab.list.df(lapply(interaction_graphs,as.data.frame))
rv_results <- statis(ig_ktab, scannf=F)
mat_plot <- rv_results$RV
colnames(mat_plot) <- translateTimes(colnames(mat_plot))
rownames(mat_plot) <- translateTimes(rownames(mat_plot))
max_value = quantile(mat_plot,0.99, na.rm=T)
mid_value = quantile(mat_plot,0.75, na.rm=T)
min_value = quantile(mat_plot,0.01, na.rm=T)
col_fun.use = colorRamp2(c(min_value,mid_value,max_value), c("#08306B","grey80","white"))
# col_fun.use = colorRamp2(breaks = c(min_value,mid_value,2), colors = c("yellow","purple","black"))
# pdf(paste0("~/Downloads/",name,".pdf"), height = 5, width = 7)
Heatmap(mat_plot, cluster_rows = F, cluster_columns = F, name = "RV\ncoef", col = col_fun.use)
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
BuildVarianceHeatmap <- function(interaction_graphs, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2",
cell.cols = NULL) {
resample <- function(x, ...) x[sample.int(length(x), ...)]
f1 <- function(lst) {
n <- length(lst)
rc <- dim(lst[[1]])
ar1 <- array(unlist(lst), c(rc, n))
var_results <- apply(ar1, c(1, 2), sd)
median_results <- apply(ar1, c(1, 2), median)
median_results <- rep(median_results,n)
time_results <- abs(ar1-median_results)
# pre_results <- rep(lst[[1]],n)
# time_results <- abs(ar1-pre_results)
time_results <- apply(time_results,c(1, 2), function(y) {resample(which(y==max(y)),1)})
time_results <- mapvalues(time_results, from = 1:n, to = names(lst))
return(list(var_results,time_results))
}
results <- f1(interaction_graphs)
var_results <- results[[1]]
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
time_results <- results[[2]]
rownames(time_results) <- rownames(interaction_graphs[[1]])
colnames(time_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
if(is.null(cell.cols)) {
cell.cols <- pal_igv()(length(unique(nbct.f$celltype)))
names(cell.cols) <- unique(nbct.f$celltype)
}
cell.cols_use <- cell.cols[names(cell.cols) %in% nbct.f$celltype]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1)),
show_legend = c(T,F))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1),
"SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,F))
}
#
max_value = quantile(var_results,0.99)
col_fun.use = colorRamp2(c(0,max_value), c("white","#08306B"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
# time_results <- translateTimes(time_results)
hc = hclust(dist(t(var_results), method="euclidean"), method = "complete")
hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
cluster_columns = hc, column_dend_reorder = F,
name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
thm <- Heatmap(time_results, name = "Timepoint",
# col = time.cols,
cluster_columns = hc, column_dend_reorder = F, show_column_dend = T,
show_row_names = F, show_column_names = F)
return(list(SCluster=row_grp,RCluster=col_grp,var_hm=hm,time_hm=thm))
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param ident.1
#' @param ident.2
#' @param row.k
#' @param col.k
#'
#' @return
#' @export
#'
#' @examples
BuildCompHeatmap <- function(interaction_graphs, seu, name = "var_results", ident.1 = NULL, ident.2 = "pre",
row.k = NULL, col.k = NULL) {
var_results <- abs(interaction_graphs[[ident.1]]-interaction_graphs[[ident.2]])
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu$celltype.l2,seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
cell.cols <- pal_igv()(length(unique(nbct.f$celltype)))
names(cell.cols) <- unique(nbct.f$celltype)
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols,
"SCluster" = row.colors))
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols,
"RCluster" = col.colors),
annotation_name_side = "left")
# pdf(paste0("~/Downloads/",name,".pdf"), height = 7, width = 9.5)
p <- Heatmap(var_results, show_row_names = T, show_column_names = T,
name = "Diff", top_annotation = ta, left_annotation = la,
row_names_gp = gpar(fontsize=0), column_names_gp = gpar(fontsize=0))
return(list(SCluster=row_grp,RCluster=col_grp,Heatmap=p))
}
#' Title
#'
#' @param seu
#' @param interactome
#' @param subset.time
#'
#' @return
#' @export
#'
#' @examples
HighlightSR <- function(seu, interactome, subset.time = NULL) {
if(!is.null(subset.time)) {
seu <- subset(seu, cells = colnames(seu)[seu$time.orig==subset.time])
message("Running PCA")
seu <- RunPCA(seu, verbose = F)
message("Running UMAP")
seu <- RunUMAP(seu, dims = 1:50, verbose = F)
}
cells = list(Senders = unique(interactome$source),
Receivers = unique(interactome$receiver))
DimPlot(seu, cells.highlight = cells, cols.highlight = list("blue","red")) + NoLegend() + theme_umap() +
labs(x = "UMAP1", y = "UMAP2")
}
#' Title
#'
#' @param connectome
#'
#' @return
#' @export
#'
#' @examples
PlotAlluviumLigRec <- function(connectome) {
connectome_plot <- connectome[,c("source_type","source","ligand","receptor","target","target_type","weight")]
colnames(connectome_plot) <- c("Sender\ncelltype","Sender\ncell","Ligand",
"Receptor","Receiver\ncell","Receiver\ncelltype","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:6, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum, fill = Weight)) +
geom_flow(stat = "alluvium", lode.guidance = "frontback",
color = "darkgray") +
geom_stratum() +
ggrepel::geom_text_repel(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6), as.character(stratum), NA)),
stat = "stratum", size = 4, direction = "y") +
theme_cowplot() + scale_fill_gradient(low = "grey50", high = "red") +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL)
}
#' Title
#'
#' @param seu
#' @param gene_rankings
#' @param interactome
#' @param min.pct
#' @param assay.use
#' @param slot.use
#' @param send_cells
#' @param rec_cells
#'
#' @return
#' @export
#'
#' @examples
PrioritizeInteractome <- function(seu, gene_rankings, interactome,
min.pct = 0.05, assay.use = "RNA", slot.use = "counts",
send_cells = NULL, rec_cells = NULL) {
if(is.null(send_cells)) {
send_cells = unique(interactome$source)
}
if(is.null(rec_cells)) {
rec_cells = unique(interactome$receiver)
}
s.exprs <- GetAssayData(seu, assay = assay.use, slot = slot.use)[,send_cells]
r.exprs <- GetAssayData(seu, assay = assay.use, slot = slot.use)[,rec_cells]
s.expressed_genes <- rownames(s.exprs)[(Matrix::rowSums(s.exprs !=0)/ncol(s.exprs))>min.pct]
r.expressed_genes <- rownames(r.exprs)[(Matrix::rowSums(r.exprs !=0)/ncol(r.exprs))>min.pct]
background_expressed_genes <- r.expressed_genes %>% .[. %in% rownames(ligand_target_matrix)]
ligands = lr_network %>% pull(from) %>% unique()
receptors = lr_network %>% pull(to) %>% unique()
expressed_ligands = intersect(ligands,s.expressed_genes)
expressed_receptors = intersect(receptors,r.expressed_genes)
potential_ligands = lr_network %>% dplyr::filter(from %in% expressed_ligands & to %in% expressed_receptors) %>% pull(from) %>% unique()
gene_rankings = gene_rankings[names(gene_rankings) %in% rec_cells]
message("Beginning NicheNet")
nichenet.results <- pblapply(gene_rankings, function(x) {
activities <- predict_ligand_activities(geneset = names(x),
ligand_target_matrix = ligand_target_matrix,
potential_ligands = potential_ligands,
background_expressed_genes = background_expressed_genes)
best_upstream_ligands = activities %>%
top_n(20, pearson) %>%
arrange(-pearson) %>%
pull(test_ligand) %>%
unique()
active_ligand_target_links_df = best_upstream_ligands %>%
lapply(get_weighted_ligand_target_links,
geneset = names(x),
ligand_target_matrix = ligand_target_matrix, n = 200) %>%
bind_rows %>% drop_na()
return(list(activities,active_ligand_target_links_df))
})
return(nichenet.results)
}
#' Title
#'
#' @param connectome
#' @param optimize.flows
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
PlotAlluvium <- function(connectome, optimize.flows = T, cell.cols = NULL) {
# if(nrow(connectome)>1e5) {
# connectome <- connectome %>% group_by(source,receiver,pair) %>% top_n(n=10,wt=target_weight)
# }
connectome_plot <- as.data.frame(connectome[,c("source_type","source","ligand","receptor","receiver","receiver_type","target","edgeweight")])
colnames(connectome_plot) <- c("Sender\ncelltype","Sender\ncell","Ligand",
"Receptor","Receiver\ncell","Receiver\ncelltype","Target\ngene","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:7, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
#to distinguish senders from receivers, so coloring doesn't fail in case the same cell is in each (we want to treat them separately)
connectome_lodes$stratum <- apply(connectome_lodes,1,function(x) {
x[4] <- ifelse(x[3]=="Sender\ncell",paste0(x[4],"_send"),x[4])
})
if(is.null(cell.cols)) {
ct <- unique(c(connectome$source_type,connectome$receiver_type))
cell.cols <- pal_igv()(length(ct))
names(cell.cols) <- ct
}
sender_fill <- cell.cols
unique_genes <- unique(c(connectome_plot$Ligand,
connectome_plot$Receptor,
connectome_plot$`Target
gene`))
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
cells <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Receiver\ncell","Sender\ncell"),"stratum"]))
senders <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Sender\ncell"),"stratum"]))
receivers <- as.character(unique(connectome_lodes[connectome_lodes$x %in% c("Receiver\ncell"),"stratum"]))
senders_weights <- aggregate(connectome_lodes[connectome_lodes$stratum %in% senders,"Weight"],by = list(connectome_lodes[connectome_lodes$stratum %in% senders,"stratum"]), sum) %>% arrange(x)
senders_fill <- colorRampPalette(c("grey80","yellow","red"))(nrow(senders_weights))
names(senders_fill) <- senders_weights$Group.1
receivers_weights <- aggregate(connectome_lodes[connectome_lodes$stratum %in% receivers,"Weight"],by = list(connectome_lodes[connectome_lodes$stratum %in% receivers,"stratum"]), sum) %>% arrange(x)
receivers_fill <- colorRampPalette(c("grey80","yellow","red"))(nrow(receivers_weights))
names(receivers_fill) <- receivers_weights$Group.1
cell_fill <- c(receivers_fill,senders_fill)
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
##attempt to make all cells equal. But I'm not sure you can (easily) or should.
##Because it's not an even mix and match between senders and receivers.
##You can scale all the senders to be the same, but that doesn't guarantee that the all the receivers will be the same, or vice versa.
# if(cells.equal){
# #calculate number of lodes per cell
# connectome_cells <- connectome_lodes[connectome_lodes$stratum %in% cells,]
# connectome_cells$stratum <- as.character(connectome_cells$stratum)
# lpc <- as.data.frame(table(connectome_cells$stratum))
# lpc$Freq <- (1/lpc$Freq)
# wpc <- unique(connectome_cells)[,c("Cohort","stratum")]
# wpc$Weight <- mapvalues(wpc$stratum, from = lpc$Var1, to = lpc$Freq)
# connectome_lodes$Weight <- mapvalues(connectome_lodes$Cohort, from = wpc$Cohort, to = wpc$Weight)
# }
# connectome_lodes$Weight <- 1
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
send_to_cell <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncelltype",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Sender\ncell",c("Cohort","x","stratum")],
by = "Cohort")
send_to_cell$stratum.x <- paste(send_to_cell$stratum.x,"send",sep = "_")
cell_to_ligand <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncell",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
by = "Cohort")
cell_to_ligand$stratum.y <- paste(cell_to_ligand$stratum.y,"ligand", sep = "_")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"receptor", sep = "_")
receptor_to_receiver <- merge(connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receiver\ncell",c("Cohort","x","stratum")],
by = "Cohort")
receptor_to_receiver$stratum.x <- paste(receptor_to_receiver$stratum.x,"receptor", sep = "_")
receiver_to_type <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncell",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
by = "Cohort")
receiver_to_type$stratum.y <- paste(receiver_to_type$stratum.y,"receiver", sep = "_")
type_to_target <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Target\ngene",c("Cohort","x","stratum")],
by = "Cohort")
type_to_target$stratum.x <- paste(type_to_target$stratum.x,"receiver", sep = "_")
type_to_target$stratum.y <- paste(type_to_target$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=send_to_cell$stratum.x,target=send_to_cell$stratum.y,value=1),
data.frame(source=cell_to_ligand$stratum.x,target=cell_to_ligand$stratum.y,value=1),
data.frame(source=ligand_to_receptor$stratum.x,target=ligand_to_receptor$stratum.y,value=1),
data.frame(source=receptor_to_receiver$stratum.x,target=receptor_to_receiver$stratum.y,value=1),
data.frame(source=receiver_to_type$stratum.x,target=receiver_to_type$stratum.y,value=1),
data.frame(source=type_to_target$stratum.x,target=type_to_target$stratum.y,value=1))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-2),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Sender\ncelltype",
paste(connectome_lodes_merge$stratum,"send",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receptor",
paste(connectome_lodes_merge$stratum,"receptor",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receiver\ncelltype",
paste(connectome_lodes_merge$stratum,"receiver",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target\ngene",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
send_fill <- sender_fill
names(send_fill) <- paste(names(send_fill),"send", sep = "_")
receiver_fill <- sender_fill
names(receiver_fill) <- paste(names(receiver_fill),"receiver", sep = "_")
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
receptor_fill <- gene_fill
names(receptor_fill) <- paste(names(receptor_fill),"receptor", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(send_fill,
receiver_fill,
ligand_fill,
receptor_fill,
target_fill,
cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(sender_fill,gene_fill,cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Title
#'
#' @param interaction_graph
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#' @param cell.cols
#'
#' @return
#' @export
#'
#' @examples
BuildSingleHeatmap <- function(interaction_graph, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2",
cell.cols = NULL) {
interaction_graph <- as.matrix(interaction_graph)
#cluster rows
message("Clustering rows")
input = interaction_graph
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward.D")
if(!is.null(row.k)) {
nclust = row.k
}
else {
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(interaction_graph)
message("Clustering columns")
#cluster columns
input = t(interaction_graph)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward.D")
if(!is.null(col.k)) {
nclust = col.k
}
else {
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(interaction_graph)
# nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
# colnames(nbct) <- c("celltype","nb","freq")
# nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
message("Building annotation")
nbct.f <- data.frame(nb=colnames(seu),celltype=seu@meta.data[,cell.type.calls]) %>%
dplyr::filter(nb %in% rownames(interaction_graph))
row.colors <- pal_igv()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_igv()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(interaction_graph),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(interaction_graph),as.character(nbct.f$nb)),]
if(is.null(cell.cols)) {
cell.cols <- pal_igv()(length(unique(seu@meta.data[,cell.type.calls])))
names(cell.cols) <- unique(seu@meta.data[,cell.type.calls])
}
cell.cols_use <- cell.cols[names(cell.cols) %in% nbct.f$celltype]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("SCluster" = row_grp,
col = list("SCluster" = row.colors),
show_legend = c(F))
ta = columnAnnotation("RCluster" = col_grp,
col = list("RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("SCluster" = row_grp,
col = list("SCluster" = row.colors),
annotation_legend_param = list("SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("RCluster" = col_grp,
col = list("RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F))
}
#
max_value = quantile(interaction_graph,0.99)
col_fun.use = colorRamp2(c(0,max_value), c("white","#08306B"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(interaction_graph, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
message("Building Heatmap")
hm <- Heatmap(interaction_graph, show_row_names = F, show_column_names = F,
name = "Interaction\nscore", top_annotation = ta, left_annotation = la, col = col_fun.use,
row_split = rowanno$celltype, column_split = colanno$celltype,
clustering_distance_rows = "euclidean", clustering_method_rows = "ward.D",
clustering_distance_columns = "euclidean", clustering_method_columns = "ward.D")
return(list(SCluster=row_grp,RCluster=col_grp,hm=hm))
}
#' Title
#'
#' @param interaction_graphs
#' @param seu
#' @param name
#' @param row.k
#' @param col.k
#' @param cell.type.calls
#'
#' @return
#' @export
#'
#' @examples
BuildGranHeatmap <- function(interaction_graphs, seu, name = "var_results",
row.k = NULL, col.k = NULL, cell.type.calls = "celltype.l2") {
resample <- function(x, ...) x[sample.int(length(x), ...)]
ig_rr <- interaction_graphs[6:9]
ig_ll <- interaction_graphs[1:5]
n <- length(ig_rr)
rc <- dim(ig_rr[[1]])
ar_rr <- array(unlist(ig_rr), c(rc, n))
n <- length(ig_ll)
rc <- dim(ig_ll[[1]])
ar_ll <- array(unlist(ig_ll), c(rc, n))
rr_mean <- apply(ar_rr, c(1, 2), mean)
ll_mean <- apply(ar_ll, c(1, 2), mean)
num <- rr_mean-ll_mean
rr_sd <- apply(ar_rr, c(1, 2), sd)
ll_sd <- apply(ar_ll, c(1, 2), sd)
rr_sd <- (rr_sd^2)/4
ll_sd <- (ll_sd^2)/5
denom <- sqrt(rr_sd+ll_sd)
var_results <- num/denom
rownames(var_results) <- rownames(interaction_graphs[[1]])
colnames(var_results) <- colnames(interaction_graphs[[1]])
#cluster rows
input = var_results
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(row.k)) {
nclust = row.k
}
row_grp <- as.character(cutree(hc1, k = nclust))
names(row_grp) <- rownames(var_results)
#cluster columns
input = t(var_results)
d <- dist(input, method = "euclidean")
hc1 <- hclust(d, method = "ward")
test <- fviz_nbclust(input, FUN = hcut, method = "wss")
nclust = elbow(test$data %>% mutate_all(as.numeric))$clusters_selected
if(!is.null(col.k)) {
nclust = col.k
}
col_grp <- as.character(cutree(hc1, k = nclust))
names(col_grp) <- colnames(var_results)
nbct <- as.data.frame(table(seu@meta.data[,cell.type.calls],seu$bins))
colnames(nbct) <- c("celltype","nb","freq")
nbct.f <- nbct %>% group_by(nb) %>% top_n(1,freq) %>% sample_n(1)
row.colors <- pal_d3()(length(unique(row_grp)))
names(row.colors) <- unique(row_grp)
col.colors <- pal_d3()(length(unique(col_grp)))
names(col.colors) <- unique(col_grp)
rowanno <- nbct.f[match(rownames(var_results),as.character(nbct.f$nb)),]
colanno <- nbct.f[match(colnames(var_results),as.character(nbct.f$nb)),]
rowanno$celltype <- factor(as.character(rowanno$celltype),
levels = unique(c(as.character(rowanno$celltype),
as.character(colanno$celltype))))
colanno$celltype <- factor(as.character(colanno$celltype),
levels = unique(c(as.character(rowanno$celltype),
as.character(colanno$celltype))))
cell.cols_use <- cell.cols[names(cell.cols) %in% levels(rowanno$celltype)]
longer = resample(which(c(length(col.colors),length(row.colors))==max(length(col.colors),length(row.colors))),1)
if(longer==1) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1)),
show_legend = c(T,F))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,T),
annotation_legend_param = list("RCluster" = list(labels = names(col.colors),
legend_gp = gpar(fill = col.colors),
title = "Cluster #")))
}
if(longer==2) {
la = rowAnnotation("Sender cell" = rowanno$celltype, "SCluster" = row_grp,
col = list("Sender cell" = cell.cols_use,
"SCluster" = row.colors),
annotation_legend_param = list("Sender cell" = list(labels = names(cell.cols_use),
legend_gp = gpar(fill = cell.cols_use),
title = "Cell type", ncol=1),
"SCluster" = list(labels = names(row.colors),
legend_gp = gpar(fill = row.colors),
title = "Cluster #")))
ta = columnAnnotation("Receiver cell" = colanno$celltype, "RCluster" = col_grp,
col = list("Receiver cell" = cell.cols_use,
"RCluster" = col.colors),
annotation_name_side = "left",
show_legend = c(F,F))
}
#
min_value = quantile(var_results,0.01)
max_value = quantile(var_results,0.99)
col_fun.use = colorRamp2(c(min_value,0,max_value), c("indianred","white","blue"))
# ct_lgd = Legend(labels = names(cell.cols), legend_gp = gpar(fill = cell.cols),
# title = "Cell type", ncol=2)
#
# cluster_lgd = Legend(labels = names(cl_cols.use), legend_gp = gpar(fill = cl_cols.use),
# title = "Cluster #")
# hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
# name = "SD", top_annotation = ta, left_annotation = la, col = col_fun.use)
#
# hm <- draw(hm)
#
# ro <- row_order(hm)
# co <- column_order(hm)
#
# time_results <- time_results[ro,co]
# time_results <- translateTimes(time_results)
hc = hclust(dist(t(var_results), method="euclidean"), method = "ward")
hc1 = hclust(dist((var_results), method="euclidean"), method = "ward")
hm <- Heatmap(var_results, show_row_names = F, show_column_names = F,
cluster_columns = hc, column_dend_reorder = F,
cluster_rows = hc1, row_dend_reorder = F,
name = "T-statistic", top_annotation = ta, left_annotation = la, col = col_fun.use)
# thm <- Heatmap(time_results,col = time.cols, name = "Timepoint",
# cluster_columns = hc, column_dend_reorder = F, show_column_dend = T,
# show_row_names = F, show_column_names = F)
return(list(SCluster=row_grp,RCluster=col_grp,var_hm=hm))
}
#' Title
#'
#' @param connectome
#' @param optimize.flows
#'
#' @return
#' @export
#'
#' @examples
PlotAlluvium_nocells <- function(connectome, optimize.flows = T) {
connectome_plot <- connectome[,c("source_type","ligand","receptor","receiver_type","target","weight")]
connectome_plot$unique <- paste(connectome_plot$source_type,
connectome_plot$ligand,
connectome_plot$receptor,
connectome_plot$receiver_type,
connectome_plot$target,
sep = "_")
connectome_plot <- aggregate(connectome_plot$weight, by = list(connectome_plot$unique), FUN = sum)
colnames(connectome_plot) <- c("unique","Weight")
connectome_plot %<>% separate(unique, into = c("source_type","ligand","receptor","receiver_type","target"), sep = "_")
colnames(connectome_plot) <- c("Sender\ncelltype","Ligand",
"Receptor","Receiver\ncelltype","Target\ngene","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:5, id = "Cohort")
connectome_lodes$stratum <- as.factor(connectome_lodes$stratum)
sender_fill <- cell.cols
unique_genes <- unique(c(connectome_plot$Ligand,
connectome_plot$Receptor,
connectome_plot$`Target
gene`))
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
send_to_ligand <- merge(connectome_lodes[connectome_lodes$x=="Sender\ncelltype",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
by = "Cohort")
send_to_ligand$stratum.x <- paste(send_to_ligand$stratum.x,"send",sep = "_")
send_to_ligand$stratum.y <- paste(send_to_ligand$stratum.y,"send",sep = "_")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"receptor", sep = "_")
receptor_to_type <- merge(connectome_lodes[connectome_lodes$x=="Receptor",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum")],
by = "Cohort")
receptor_to_type$stratum.x <- paste(receptor_to_type$stratum.x,"receiver", sep = "_")
receptor_to_type$stratum.y <- paste(receptor_to_type$stratum.y,"receiver", sep = "_")
type_to_target <- merge(connectome_lodes[connectome_lodes$x=="Receiver\ncelltype",c("Cohort","x","stratum","Weight")],
connectome_lodes[connectome_lodes$x=="Target\ngene",c("Cohort","x","stratum")],
by = "Cohort")
type_to_target$stratum.x <- paste(type_to_target$stratum.x,"receiver", sep = "_")
type_to_target$stratum.y <- paste(type_to_target$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=send_to_ligand$stratum.x,target=send_to_ligand$stratum.y,value=send_to_ligand$Weight),
data.frame(source=ligand_to_receptor$stratum.x,target=ligand_to_receptor$stratum.y,value=ligand_to_receptor$Weight),
data.frame(source=receptor_to_type$stratum.x,target=receptor_to_type$stratum.y,value=receptor_to_type$Weight),
data.frame(source=type_to_target$stratum.x,target=type_to_target$stratum.y,value=type_to_target$Weight))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(plyr::mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(plyr::mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-2),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Sender\ncelltype",
paste(connectome_lodes_merge$stratum,"send",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receptor",
paste(connectome_lodes_merge$stratum,"receptor",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Receiver\ncelltype",
paste(connectome_lodes_merge$stratum,"receiver",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target\ngene",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
send_fill <- sender_fill
names(send_fill) <- paste(names(send_fill),"send", sep = "_")
receiver_fill <- sender_fill
names(receiver_fill) <- paste(names(receiver_fill),"receiver", sep = "_")
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
receptor_fill <- gene_fill
names(receptor_fill) <- paste(names(receptor_fill),"receptor", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(stat = "alluvium", lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
geom_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(send_fill,
receiver_fill,
ligand_fill,
receptor_fill,
target_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1:5), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(sender_fill,gene_fill,cell_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,3,4,6,7), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Title
#'
#' @param ccim
#' @param seu
#' @param features
#' @param type_plot
#' @param ...
#'
#' @return
#' @import magrittr
#' @export
#'
#' @examples
CCIMFeaturePlot <- function(ccim, seu,
features = NULL,
type_plot = c("sender","receiver"), ...) {
#find cells of interest in the original object
type_plot <- match.arg(arg = type_plot, several.ok = F)
p <- FeaturePlot(seu, features = features, combine = F)
if(length(features)>1) {
pdata <- as.data.frame(t(do.call(rbind,lapply(p,function(x) {x$data[,4]}))))
colnames(pdata) <- features
rownames(pdata) <- colnames(seu)
}
else {
pdata <- as.data.frame(x=p[[1]]$data[,4])
colnames(pdata) <- features
rownames(pdata) <- colnames(seu)
}
ccim_meta <- merge((ccim@meta.data %>% rownames_to_column("cell")),
(pdata %>% rownames_to_column(type_plot)),
by = type_plot, all.y = F)
ccim_meta <- ccim_meta[match(colnames(ccim),ccim_meta$cell),]
rownames(ccim_meta) <- NULL
ccim_meta %<>%
column_to_rownames("cell")
ccim@meta.data <- ccim_meta
FeaturePlot(ccim, features = features, ... )
}
#' Plot expression of interaction programs
#'
#' @param seu A seurat object that has interaction program expression information stored in the meta.data slot as the output of `ScoreInteractionPrograms`
#' @param ip The name of the interaction program to plot
#' @param cols Character vector of colors to use for plotting
#' @param order Logical. Order points so highest expressers are on top?
#'
#' @return
#' @import ggplot2
#' @export
#'
#' @examples
IPFeaturePlot <- function(seu, ip, cols = c("grey90","blue","orangered3"), order = T) {
seu$lig_feature <- seu[["IPligands"]]@data[ip,]
seu$rec_feature <- seu[["IPreceptors"]]@data[ip,]
# p <- FeaturePlot(seu,
# features = c(paste0("ligands_",ip),
# paste0("receptors_",ip)),
# blend = T, combine = F,
# cols = cols, order = order)
p <- FeaturePlot(seu,
features = c("lig_feature","rec_feature"),
blend = T, combine = F,
cols = cols, order = order)
p[[3]] + NoLegend() + labs(x = NULL, y = NULL, title = NULL) +
theme(aspect.ratio = 1,axis.ticks = element_blank(),
axis.text = element_blank())
}
#' Plot Alluvial of ligand-target links
#'
#' @param connectome
#' @param optimize.flows
#' @param colors
#'
#' @return
#' @export
#'
#' @examples
PlotAlluviumLT <- function(connectome, optimize.flows = T, colors = NULL) {
connectome_plot <- as.data.frame(connectome[,c("ligand","target","mean")])
colnames(connectome_plot) <- c("Ligand","Target","Weight")
connectome_lodes <- to_lodes_form(connectome_plot, axes = 1:2, id = "Cohort")
connectome_lodes$stratum <- as.character(connectome_lodes$stratum)
if(is.null(colors)) {
unique_genes <- unique(connectome_lodes$stratum)
gene_fill <- hue_pal()(length(unique_genes))
names(gene_fill) <- unique_genes
}
else {
gene_fill <- colors
}
if(optimize.flows) {
message("Preparing data for networkD3 . . . ")
ligand_to_receptor <- merge(connectome_lodes[connectome_lodes$x=="Ligand",c("Cohort","x","stratum")],
connectome_lodes[connectome_lodes$x=="Target",c("Cohort","x","stratum")],
by = "Cohort")
ligand_to_receptor$stratum.x <- paste(ligand_to_receptor$stratum.x,"ligand", sep = "_")
ligand_to_receptor$stratum.y <- paste(ligand_to_receptor$stratum.y,"target", sep = "_")
links <- rbind(data.frame(source=ligand_to_receptor$stratum.x,
target=ligand_to_receptor$stratum.y,value=1))
node.list <- unique(c(links$source,links$target))
nodes <- data.frame(node = 1:length(unique(node.list)), name = unique(node.list))
nodes$node <- nodes$node-1
links$source <- as.numeric(mapvalues(links$source, from = nodes$name, to = nodes$node, warn_missing = F))
links$target <- as.numeric(mapvalues(links$target, from = nodes$name, to = nodes$node, warn_missing = F))
p1 <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize = 12, nodeWidth = 30)
customJS <- 'function() { console.log(this.sankey.nodes().map(d => [d.name, d.x, d.y])); }'
p2 <- htmlwidgets::onRender(p1, customJS)
saveNetwork(p2, "~/Downloads/sankey_networkD3.html")
browseURL('file:///Users/aaronwilk/Downloads/sankey_networkD3.html')
message("Please browse the code for the opened Sankey diagram (control-command-C)
Navigate to the console tab and copy the contents of this tab
Type 'yes' below when this has been completed.\n
If you are prompted more than once, try copying again, you probably copied without the line breaks")
status <- "no"
while(status!="yes") {
status <- readline(prompt = "Have node positions been copied?: ")
nodePositions <- read_clip_tbl()
nodePositions <- data.frame(x=nodePositions[!grepl("^\\[",nodePositions[,1]),])
status <- ifelse(nrow(nodePositions)>1,"yes","no")
}
# nodePositions <- read.csv("~/Downloads/nodePositions.csv")
colnames(nodePositions) <- "x_axis"
nodePositions$x_axis <- sub("\\].*", "", sub(".*\\[", "", nodePositions$x_axis))
nodePositions <- as.data.frame(t(as.data.frame(str_split(nodePositions$x_axis,","))))
rownames(nodePositions) <- NULL
colnames(nodePositions) <- c("stratum_full","x_axis","y")
nodePositions <- nodePositions[1:(nrow(nodePositions)-1),]
trim.leading <- function (x) sub("^\\s+", "", x)
nodePositions$x_axis <- as.numeric(trim.leading(nodePositions$x_axis))
nodePositions$y <- as.numeric(trim.leading(nodePositions$y))
nodePositions$stratum_full <- gsub("'","",nodePositions$stratum_full)
nodePositions$x_axis <- scales::rescale(nodePositions$x_axis, newrange = c(0,10*max(nodePositions$y)))
nodePositions$num_rank <- nodePositions$x_axis+nodePositions$y
nodePositions %<>%
mutate(rank = order(order(num_rank, decreasing = F)))
new.levels <- nodePositions %>% arrange(num_rank) %>% pull(stratum_full)
connectome_lodes_merge <- connectome_lodes
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Ligand",
paste(connectome_lodes_merge$stratum,"ligand",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- ifelse(connectome_lodes_merge$x=="Target",
paste(connectome_lodes_merge$stratum,"target",sep = "_"),
connectome_lodes_merge$stratum)
connectome_lodes_merge$stratum <- factor(connectome_lodes_merge$stratum, levels = new.levels)
ligand_fill <- gene_fill
names(ligand_fill) <- paste(names(ligand_fill),"ligand", sep = "_")
target_fill <- gene_fill
names(target_fill) <- paste(names(target_fill),"target", sep = "_")
ggplot(connectome_lodes_merge, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(ligand_fill,
target_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,2), sub("_[^_]+$", "", stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
else {
ggplot(connectome_lodes, aes(x = x, stratum = stratum, alluvium = Cohort,
y = Weight, label = stratum)) +
geom_flow(lode.guidance = "frontback",color = "darkgray",cement.alluvia = T) +
stat_stratum(aes(fill = stratum), width = 1/3) + scale_fill_manual(values = c(gene_fill)) +
ggfittext::geom_fit_text(aes(label = ifelse(as.numeric(x) %in% c(1,2), as.character(stratum), NA)),
stat = "stratum", width = 1/3, min.size = 3) +
theme_cowplot() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank()) + labs(x = NULL) + NoLegend()
}
}
#' Plot Pearson distributions for ligand activities
#'
#' @param ligand_activities the matrix output of `RankActiveLigands`
#' @param pearson_cutoff determines where to draw a vertical line illustrating the chosen Pearson threshold cutoff (default: 0.075)
#'
#' @return Two plots of all Pearson coefficients (left) and median Pearson coefficient per cell (right)
#' @export
#'
#' @examples
PearsonDist <- function(ligand_activities, pearson_cutoff = 0.075) {
ral_df <- data.frame(x = as.vector(ligand_activities))
minx <- min(ral_df$x)
maxx <- max(ral_df$x)
p1 <- ggplot(ral_df, aes(x = x)) + geom_density(fill = "steelblue") + theme_cowplot() +
labs(x = "Pearson coefficient", y = "Density", title = "All Pearson coefficients") +
xlim(c(minx,maxx)) + geom_vline(xintercept = pearson_cutoff) +
theme(plot.title = element_text(hjust = 0.5), aspect.ratio = 1)
ral_df <- data.frame(x = as.vector(apply(ligand_activities,2,median)))
p2 <- ggplot(ral_df, aes(x = x)) + geom_density(fill = "steelblue") + theme_cowplot() +
labs(x = "Pearson coefficient", y = "Density", title = "Median Pearson coefficient\nper cell") +
xlim(c(minx,maxx)) + geom_vline(xintercept = pearson_cutoff) +
theme(plot.title = element_text(hjust = 0.5), aspect.ratio = 1)
p1|p2
}
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