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visualization.R
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#' ggplot theme in CellChat
#'
#' @return
#' @export
#'
#' @examples
#' @importFrom ggplot2 theme_classic element_rect theme element_blank element_line element_text
CellChat_theme_opts <- function() {
theme(strip.background = element_rect(colour = "white", fill = "white")) +
theme_classic() +
theme(panel.border = element_blank()) +
theme(axis.line.x = element_line(color = "black")) +
theme(axis.line.y = element_line(color = "black")) +
theme(panel.grid.minor.x = element_blank(), panel.grid.minor.y = element_blank()) +
theme(panel.grid.major.x = element_blank(), panel.grid.major.y = element_blank()) +
theme(panel.background = element_rect(fill = "white")) +
theme(legend.key = element_blank()) + theme(plot.title = element_text(size = 10, face = "bold", hjust = 0.5))
}
#' Generate ggplot2 colors
#'
#' @param n number of colors to generate
#' @importFrom grDevices hcl
#' @export
#'
ggPalette <- function(n) {
hues = seq(15, 375, length = n + 1)
grDevices::hcl(h = hues, l = 65, c = 100)[1:n]
}
#' Generate colors from a customed color palette
#'
#' @param n number of colors
#'
#' @return A color palette for plotting
#' @importFrom grDevices colorRampPalette
#'
#' @export
#'
scPalette <- function(n) {
colorSpace <- c('#E41A1C','#377EB8','#4DAF4A','#984EA3','#F29403','#F781BF','#BC9DCC','#A65628','#54B0E4','#222F75','#1B9E77','#B2DF8A',
'#E3BE00','#FB9A99','#E7298A','#910241','#00CDD1','#A6CEE3','#CE1261','#5E4FA2','#8CA77B','#00441B','#DEDC00','#DCF0B9','#8DD3C7','#999999')
if (n <= length(colorSpace)) {
colors <- colorSpace[1:n]
} else {
colors <- grDevices::colorRampPalette(colorSpace)(n)
}
return(colors)
}
#' Visualize the inferred cell-cell communication network
#'
#' Automatically save plots in the current working directory.
#'
#' @param object CellChat object
#' @param signaling a signaling pathway name
#' @param signaling.name alternative signaling pathway name to show on the plot
#' @param color.use the character vector defining the color of each cell group
#' @param vertex.receiver a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
#' @param top the fraction of interactions to show (0 < top <= 1)
#' @param sources.use a vector giving the index or the name of source cell groups
#' @param targets.use a vector giving the index or the name of target cell groups.
#' @param remove.isolate whether remove the isolate nodes in the communication network
#' @param weight.scale whether scale the edge weight
#' @param vertex.weight The weight of vertex: either a scale value or a vector
#'
#' Default is a scale value being 1, indicating all vertex is plotted in the same size;
#'
#' Set `vertex.weight` as a vector to plot vertex in different size; setting `vertex.weight = NULL` will have vertex with different size that are portional to the number of cells in each cell group.
#'
#' @param vertex.weight.max the maximum weight of vertex; defualt = max(vertex.weight)
#' @param vertex.size.max the maximum vertex size for visualization
#' @param edge.weight.max.individual the maximum weight of edge when plotting the individual L-R netwrok; defualt = max(net)
#' @param edge.weight.max.aggregate the maximum weight of edge when plotting the aggregated signaling pathway network
#' @param edge.width.max The maximum edge width for visualization
#' @param layout "hierarchy", "circle" or "chord"
#' @param height height of plot
#' @param thresh threshold of the p-value for determining significant interaction
#' @param pt.title font size of the text
#' @param title.space the space between the title and plot
#' @param vertex.label.cex The label size of vertex in the network
#' @param out.format the format of output figures: svg, png and pdf
#'
#' Parameters below are set for "spatial" diagram. Please also check the function `netVisual_spatial` for more parameters.
#' @param sample.use the sample used for visualization, which should be the element in `object@meta$samples`.
#' @param alpha.image the transparency of individual spots
#' @param point.size the size of spots
#'
#' @param from,to,bidirection Deprecated. Use `sources.use`,`targets.use`
#' @param vertex.size Deprecated. Use `vertex.weight`
#'
#' Parameters below are set for "chord" diagram. Please also check the function `netVisual_chord_cell` for more parameters.
#' @param group A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector.
#' The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups.
#' @param cell.order a char vector defining the cell type orders (sector orders)
#' @param small.gap Small gap between sectors.
#' @param big.gap Gap between the different sets of sectors, which are defined in the `group` parameter
#' @param scale scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
#' @param reduce if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid.
#' @param show.legend whether show the figure legend
#' @param legend.pos.x,legend.pos.y adjust the legend position
#' @param nCol number of columns when displaying the network mediated by ligand-receptor using "circle" or "chord"
#'
#' @param ... other parameters (e.g.,vertex.label.cex, vertex.label.color, alpha.edge, label.edge, edge.label.color, edge.label.cex, edge.curved, text.x, text.y)
#' passing to `netVisual_hierarchy1`,`netVisual_hierarchy2`,`netVisual_circle`. NB: some parameters might be not supported
#' @importFrom svglite svglite
#' @importFrom grDevices dev.off pdf
#'
#' @return
#' @export
#'
#' @examples
#'
netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL, vertex.receiver = NULL, sources.use = NULL, targets.use = NULL, top = 1, remove.isolate = FALSE,
vertex.weight = 1, vertex.weight.max = NULL, vertex.size.max = NULL,
weight.scale = TRUE, edge.weight.max.individual = NULL, edge.weight.max.aggregate = NULL, edge.width.max=8,
layout = c("circle","hierarchy","chord","spatial"), height = 5, thresh = 0.05, pt.title = 12, title.space = 6, vertex.label.cex = 0.8,from = NULL, to = NULL, bidirection = NULL,vertex.size = NULL,
out.format = c("svg","png"),
sample.use = NULL, alpha.image = 0.15, point.size = 1.5,
group = NULL,cell.order = NULL,small.gap = 1, big.gap = 10, scale = FALSE, reduce = -1, show.legend = FALSE, legend.pos.x = 20,legend.pos.y = 20, nCol = NULL,
...) {
layout <- match.arg(layout)
if (!is.null(vertex.size)) {
warning("'vertex.size' is deprecated. Use `vertex.weight`")
}
if (is.null(vertex.weight)) {
vertex.weight <- as.numeric(table(object@idents))
}
if (is.null(vertex.size.max)) {
if (length(unique(vertex.weight)) == 1) {
vertex.size.max <- 5
} else {
vertex.size.max <- 15
}
}
pairLR <- searchPair(signaling = signaling, pairLR.use = object@LR$LRsig, key = "pathway_name", matching.exact = T, pair.only = F)
if (is.null(signaling.name)) {
signaling.name <- signaling
}
net <- object@net
pairLR.use.name <- dimnames(net$prob)[[3]]
pairLR.name <- intersect(rownames(pairLR), pairLR.use.name)
pairLR <- pairLR[pairLR.name, ]
prob <- net$prob
pval <- net$pval
prob[pval > thresh] <- 0
if (length(pairLR.name) > 1) {
pairLR.name.use <- pairLR.name[apply(prob[,,pairLR.name], 3, sum) != 0]
} else {
pairLR.name.use <- pairLR.name[sum(prob[,,pairLR.name]) != 0]
}
if (length(pairLR.name.use) == 0) {
stop(paste0('There is no significant communication of ', signaling.name))
} else {
pairLR <- pairLR[pairLR.name.use,]
}
nRow <- length(pairLR.name.use)
prob <- prob[,,pairLR.name.use]
pval <- pval[,,pairLR.name.use]
if (is.null(nCol)) {
nCol <- min(length(pairLR.name.use), 2)
}
if (length(dim(prob)) == 2) {
prob <- replicate(1, prob, simplify="array")
pval <- replicate(1, pval, simplify="array")
}
# prob <-(prob-min(prob))/(max(prob)-min(prob))
if (is.null(edge.weight.max.individual)) {
edge.weight.max.individual = max(prob)
}
prob.sum <- apply(prob, c(1,2), sum)
# prob.sum <-(prob.sum-min(prob.sum))/(max(prob.sum)-min(prob.sum))
if (is.null(edge.weight.max.aggregate)) {
edge.weight.max.aggregate = max(prob.sum)
}
if (layout == "hierarchy") {
if (is.element("svg", out.format)) {
svglite::svglite(file = paste0(signaling.name, "_hierarchy_individual.svg"), width = 8, height = nRow*height)
par(mfrow=c(nRow,2), mar = c(5, 4, 4, 2) +0.1)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_hierarchy1(prob.i, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.i, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name, "_hierarchy_individual.png"), width = 8, height = nRow*height, units = "in",res = 300)
par(mfrow=c(nRow,2), mar = c(5, 4, 4, 2) +0.1)
for (i in 1:length(pairLR.name.use)) {
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_hierarchy1(prob.i, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.i, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max =edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name, "_hierarchy_individual.pdf"), width = 8, height = nRow*height)
grDevices::cairo_pdf(paste0(signaling.name, "_hierarchy_individual.pdf"), width = 8, height = nRow*height)
par(mfrow=c(nRow,2), mar = c(5, 4, 4, 2) +0.1)
for (i in 1:length(pairLR.name.use)) {
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_hierarchy1(prob.i, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.i, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max =edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("svg", out.format)) {
svglite::svglite(file = paste0(signaling.name, "_hierarchy_aggregate.svg"), width = 7, height = 1*height)
par(mfrow=c(1,2), ps = pt.title)
netVisual_hierarchy1(prob.sum, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max,title.name = NULL, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.sum, vertex.receiver = setdiff(1:nrow(prob.sum),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max,title.name = NULL, vertex.label.cex = vertex.label.cex,...)
graphics::mtext(paste0(signaling.name, " signaling pathway network"), side = 3, outer = TRUE, cex = 1, line = -title.space)
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name, "_hierarchy_aggregate.png"), width = 7, height = 1*height, units = "in",res = 300)
par(mfrow=c(1,2), ps = pt.title)
netVisual_hierarchy1(prob.sum, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max, title.name = NULL, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.sum, vertex.receiver = setdiff(1:nrow(prob.sum),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max,title.name = NULL, vertex.label.cex = vertex.label.cex,...)
graphics::mtext(paste0(signaling.name, " signaling pathway network"), side = 3, outer = TRUE, cex = 1, line = -title.space)
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name, "_hierarchy_aggregate.pdf"), width = 7, height = 1*height)
grDevices::cairo_pdf(paste0(signaling.name, "_hierarchy_aggregate.pdf"), width = 7, height = 1*height)
par(mfrow=c(1,2), ps = pt.title)
netVisual_hierarchy1(prob.sum, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max, title.name = NULL, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.sum, vertex.receiver = setdiff(1:nrow(prob.sum),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max, title.name = NULL, vertex.label.cex = vertex.label.cex,...)
graphics::mtext(paste0(signaling.name, " signaling pathway network"), side = 3, outer = TRUE, cex = 1, line = -title.space)
dev.off()
}
} else if (layout == "circle") {
if (is.element("svg", out.format)) {
svglite::svglite(file = paste0(signaling.name,"_", layout, "_individual.svg"), width = height, height = nRow*height)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_circle(prob.i, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_individual.png"), width = height, height = nRow*height, units = "in",res = 300)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_circle(prob.i, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_circle(prob.i, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max,title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
# prob.sum <- apply(prob, c(1,2), sum)
# prob.sum <-(prob.sum-min(prob.sum))/(max(prob.sum)-min(prob.sum))
if (is.element("svg", out.format)) {
svglite(file = paste0(signaling.name,"_", layout, "_aggregate.svg"), width = height, height = 1*height)
netVisual_circle(prob.sum, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_aggregate.png"), width = height, height = 1*height, units = "in",res = 300)
netVisual_circle(prob.sum, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
netVisual_circle(prob.sum, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.aggregate, edge.width.max=edge.width.max, title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
} else if (layout == "spatial") {
coordinates <- object@images$coordinates
labels <- object@idents
meta.t <- object@meta
meta.t$labels <- labels
if (is.element("svg", out.format)) {
svglite::svglite(file = paste0(signaling.name,"_", layout, "_individual.svg"), width = height, height = nRow*height)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_spatial(prob.i, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_individual.png"), width = height, height = nRow*height, units = "in",res = 300)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_spatial(prob.i, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
# par(mfrow=c(nRow,1))
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
for (i in 1:length(pairLR.name.use)) {
#signalName_i <- paste0(pairLR$ligand[i], "-",pairLR$receptor[i], sep = "")
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_spatial(prob.i, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
# prob.sum <- apply(prob, c(1,2), sum)
# prob.sum <-(prob.sum-min(prob.sum))/(max(prob.sum)-min(prob.sum))
if (is.element("svg", out.format)) {
svglite(file = paste0(signaling.name,"_", layout, "_aggregate.svg"), width = height, height = 1*height)
netVisual_spatial(prob.sum, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_aggregate.png"), width = height, height = 1*height, units = "in",res = 300)
netVisual_spatial(prob.sum, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
netVisual_spatial(prob.sum, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
dev.off()
}
} else if (layout == "chord") {
if (is.element("svg", out.format)) {
svglite::svglite(file = paste0(signaling.name,"_", layout, "_individual.svg"), width = height, height = nRow*height)
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
# gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
title.name <- pairLR$interaction_name_2[i]
net <- prob[,,i]
netVisual_chord_cell_internal(net, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = title.name, show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
}
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_individual.png"), width = height, height = nRow*height, units = "in",res = 300)
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
# gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
title.name <- pairLR$interaction_name_2[i]
net <- prob[,,i]
netVisual_chord_cell_internal(net, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = title.name, show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
}
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_individual.pdf"), width = height, height = nRow*height)
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
# gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
title.name <- pairLR$interaction_name_2[i]
net <- prob[,,i]
netVisual_chord_cell_internal(net, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = title.name, show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
}
dev.off()
}
# prob.sum <- apply(prob, c(1,2), sum)
if (is.element("svg", out.format)) {
svglite(file = paste0(signaling.name,"_", layout, "_aggregate.svg"), width = height, height = 1*height)
netVisual_chord_cell_internal(prob.sum, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = paste0(signaling.name, " signaling pathway network"), show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
dev.off()
}
if (is.element("png", out.format)) {
grDevices::png(paste0(signaling.name,"_", layout, "_aggregate.png"), width = height, height = 1*height, units = "in",res = 300)
netVisual_chord_cell_internal(prob.sum, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = paste0(signaling.name, " signaling pathway network"), show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
dev.off()
}
if (is.element("pdf", out.format)) {
# grDevices::pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
grDevices::cairo_pdf(paste0(signaling.name,"_", layout, "_aggregate.pdf"), width = height, height = 1*height)
netVisual_chord_cell_internal(prob.sum, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = paste0(signaling.name, " signaling pathway network"), show.legend = show.legend, legend.pos.x = legend.pos.x,legend.pos.y=legend.pos.y)
dev.off()
}
}
}
#' Visualize the inferred signaling network of signaling pathways by aggregating all L-R pairs
#'
#' @param object CellChat object
#' @param signaling a signaling pathway name
#' @param signaling.name alternative signaling pathway name to show on the plot
#' @param color.use the character vector defining the color of each cell group
#' @param vertex.receiver a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
#' @param sources.use a vector giving the index or the name of source cell groups
#' @param targets.use a vector giving the index or the name of target cell groups.
#' @param idents.use a vector giving the index or the name of cell groups of interest.
#' @param remove.isolate whether remove the isolate nodes in the communication network
#' @param top the fraction of interactions to show
#' @param weight.scale whether scale the edge weight
#' @param vertex.weight The weight of vertex: either a scale value or a vector
#'
#' Default is a scale value being 1, indicating all vertex is plotted in the same size;
#'
#' Set `vertex.weight` as a vector to plot vertex in different size; setting `vertex.weight = NULL` will have vertex with different size that are portional to the number of cells in each cell group.
#'
#' @param vertex.weight.max the maximum weight of vertex; defualt = max(vertex.weight)
#' @param vertex.size.max the maximum vertex size for visualization
#' @param edge.weight.max the maximum weight of edge; defualt = max(net)
#' @param edge.width.max The maximum edge width for visualization
#' @param layout "hierarchy", "circle", "chord" or "spatial"
#' @param thresh threshold of the p-value for determining significant interaction
#' @param pt.title font size of the text
#' @param title.space the space between the title and plot
#' @param vertex.label.cex The label size of vertex in the network
#'
#' Parameters below are set for "spatial" diagram. Please also check the function `netVisual_spatial` for more parameters.
#' @param sample.use the sample used for visualization, which should be the element in `object@meta$samples`.
#' @param alpha.image the transparency of individual spots
#' @param point.size the size of spots
#'
#' Parameters below are set for "chord" diagram. Please also check the function `netVisual_chord_cell` for more parameters.
#' @param group A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector.
#' The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups.
#' @param cell.order a char vector defining the cell type orders (sector orders)
#' @param small.gap Small gap between sectors.
#' @param big.gap Gap between the different sets of sectors, which are defined in the `group` parameter
#' @param scale scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
#' @param reduce if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid.
#' @param show.legend whether show the figure legend
#' @param legend.pos.x,legend.pos.y adjust the legend position
#'
#' @param ... other parameters (e.g.,vertex.label.cex, vertex.label.color, alpha.edge, label.edge, edge.label.color, edge.label.cex, edge.curved, text.x,text.y)
#' passing to `netVisual_hierarchy1`,`netVisual_hierarchy2`,`netVisual_circle`,`netVisual_spatial`. NB: some parameters might be not supported
#' @importFrom grDevices recordPlot
#'
#' @return an object of class "recordedplot" or ggplot
#' @export
#'
#'
netVisual_aggregate <- function(object, signaling, signaling.name = NULL, color.use = NULL, thresh = 0.05, vertex.receiver = NULL, sources.use = NULL, targets.use = NULL, idents.use = NULL, top = 1, remove.isolate = FALSE,
vertex.weight = 1, vertex.weight.max = NULL, vertex.size.max = NULL,
weight.scale = TRUE, edge.weight.max = NULL, edge.width.max=8,
layout = c("circle","hierarchy","chord","spatial"),
pt.title = 12, title.space = 6, vertex.label.cex = 0.8,
sample.use = NULL, alpha.image = 0.15, point.size = 1.5,
group = NULL,cell.order = NULL,small.gap = 1, big.gap = 10, scale = FALSE, reduce = -1, show.legend = FALSE, legend.pos.x = 20,legend.pos.y = 20,
...) {
layout <- match.arg(layout)
if (is.null(vertex.weight)) {
vertex.weight <- as.numeric(table(object@idents))
}
if (is.null(vertex.size.max)) {
if (length(unique(vertex.weight)) == 1) {
vertex.size.max <- 5
} else {
vertex.size.max <- 15
}
}
pairLR <- searchPair(signaling = signaling, pairLR.use = object@LR$LRsig, key = "pathway_name", matching.exact = T, pair.only = T)
if (is.null(signaling.name)) {
signaling.name <- signaling
}
net <- object@net
pairLR.use.name <- dimnames(net$prob)[[3]]
pairLR.name <- intersect(rownames(pairLR), pairLR.use.name)
pairLR <- pairLR[pairLR.name, ]
prob <- net$prob
pval <- net$pval
prob[pval > thresh] <- 0
if (length(pairLR.name) > 1) {
pairLR.name.use <- pairLR.name[apply(prob[,,pairLR.name], 3, sum) != 0]
} else {
pairLR.name.use <- pairLR.name[sum(prob[,,pairLR.name]) != 0]
}
if (length(pairLR.name.use) == 0) {
stop(paste0('There is no significant communication of ', signaling.name))
} else {
pairLR <- pairLR[pairLR.name.use,]
}
nRow <- length(pairLR.name.use)
prob <- prob[,,pairLR.name.use]
pval <- pval[,,pairLR.name.use]
if (length(dim(prob)) == 2) {
prob <- replicate(1, prob, simplify="array")
pval <- replicate(1, pval, simplify="array")
}
# prob <-(prob-min(prob))/(max(prob)-min(prob))
if (layout == "hierarchy") {
prob.sum <- apply(prob, c(1,2), sum)
# prob.sum <-(prob.sum-min(prob.sum))/(max(prob.sum)-min(prob.sum))
if (is.null(edge.weight.max)) {
edge.weight.max = max(prob.sum)
}
par(mfrow=c(1,2), ps = pt.title)
netVisual_hierarchy1(prob.sum, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max, title.name = NULL, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.sum, vertex.receiver = setdiff(1:nrow(prob.sum),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max, title.name = NULL, vertex.label.cex = vertex.label.cex,...)
graphics::mtext(paste0(signaling.name, " signaling pathway network"), side = 3, outer = TRUE, cex = 1, line = -title.space)
# https://www.andrewheiss.com/blog/2016/12/08/save-base-graphics-as-pseudo-objects-in-r/
# grid.echo()
# gg <- grid.grab()
gg <- recordPlot()
} else if (layout == "circle") {
prob.sum <- apply(prob, c(1,2), sum)
# prob.sum <-(prob.sum-min(prob.sum))/(max(prob.sum)-min(prob.sum))
gg <- netVisual_circle(prob.sum, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
} else if (layout == "spatial") {
prob.sum <- apply(prob, c(1,2), sum)
if (vertex.weight == "incoming"){
if (length(slot(object, "netP")$centr) == 0) {
stop("Please run `netAnalysis_computeCentrality` to compute the network centrality scores! ")
}
vertex.weight = object@netP$centr[[signaling]]$indeg
} else if (vertex.weight == "outgoing"){
if (length(slot(object, "netP")$centr) == 0) {
stop("Please run `netAnalysis_computeCentrality` to compute the network centrality scores! ")
}
vertex.weight = object@netP$centr[[signaling]]$outdeg
}
coordinates <- object@images$coordinates
labels <- object@idents
meta.t <- object@meta
meta.t$labels <- labels
gg <- netVisual_spatial(prob.sum, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = paste0(signaling.name, " signaling pathway network"), vertex.label.cex = vertex.label.cex,...)
} else if (layout == "chord") {
prob.sum <- apply(prob, c(1,2), sum)
gg <- netVisual_chord_cell_internal(prob.sum, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = paste0(signaling.name, " signaling pathway network"), show.legend = show.legend, legend.pos.x = legend.pos.x, legend.pos.y= legend.pos.y)
}
return(gg)
}
#' Visualize the inferred signaling network of individual L-R pairs
#'
#' @param object CellChat object
#' @param signaling a signaling pathway name
#' @param signaling.name alternative signaling pathway name to show on the plot
#' @param pairLR.use a char vector or a data frame consisting of one column named "interaction_name", defining the L-R pairs of interest
#' @param color.use the character vector defining the color of each cell group
#' @param vertex.receiver a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
#' @param sources.use a vector giving the index or the name of source cell groups
#' @param targets.use a vector giving the index or the name of target cell groups.
#' @param remove.isolate whether remove the isolate nodes in the communication network
#' @param top the fraction of interactions to show
#' @param weight.scale whether scale the edge weight
#' @param vertex.weight The weight of vertex: either a scale value or a vector.
#'
#' Default is a scale value being 1, indicating all vertex is plotted in the same size;
#'
#' Set `vertex.weight` as a vector to plot vertex in different size; setting `vertex.weight = NULL` will have vertex with different size that are portional to the number of cells in each cell group.
#'
#' @param vertex.weight.max the maximum weight of vertex; defualt = max(vertex.weight)
#' @param vertex.size.max the maximum vertex size for visualization
#' @param vertex.label.cex The label size of vertex in the network
#' @param edge.weight.max the maximum weight of edge; defualt = max(net)
#' @param edge.width.max The maximum edge width for visualization
#' @param graphics.init whether do graphics initiation using par(...). If graphics.init=FALSE, USERS can use par() in a more fexible way
#' @param layout "hierarchy", "circle" or "chord"
#' @param height height of plot
#' @param thresh threshold of the p-value for determining significant interaction
# #' @param from,to,bidirection Deprecated. Use `sources.use`,`targets.use`
# #' @param vertex.size Deprecated. Use `vertex.weight`
#' Parameters below are set for "spatial" diagram. Please also check the function `netVisual_spatial` for more parameters.
#' @param alpha.image the transparency of individual spots
#' @param point.size the size of spots
#'
#' Parameters below are set for "chord" diagram. Please also check the function `netVisual_chord_cell` for more parameters.
#' @param group A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector.
#' The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups.
#' @param cell.order a char vector defining the cell type orders (sector orders)
#' @param small.gap Small gap between sectors.
#' @param big.gap Gap between the different sets of sectors, which are defined in the `group` parameter
#' @param scale scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
#' @param reduce if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid.
#' @param show.legend whether show the figure legend
#' @param legend.pos.x,legend.pos.y adjust the legend position
#' @param nCol number of columns when displaying the figures using "circle" or "chord"
#'
#' @param ... other parameters (e.g.,vertex.label.cex, vertex.label.color, alpha.edge, label.edge, edge.label.color, edge.label.cex, edge.curved, text.x, text.y)
#' passing to `netVisual_hierarchy1`,`netVisual_hierarchy2`,`netVisual_circle`. NB: some parameters might be not supported
#' @importFrom grDevices dev.off pdf
#'
#' @return an object of class "recordedplot"
#' @export
#'
#'
netVisual_individual <- function(object, signaling, signaling.name = NULL, pairLR.use = NULL, color.use = NULL, vertex.receiver = NULL, sources.use = NULL, targets.use = NULL, top = 1, remove.isolate = FALSE,
vertex.weight = 1, vertex.weight.max = NULL, vertex.size.max = NULL, vertex.label.cex = 0.8,
weight.scale = TRUE, edge.weight.max = NULL, edge.width.max=8, graphics.init = TRUE,
layout = c("circle","hierarchy","chord","spatial"), height = 5, thresh = 0.05, #from = NULL, to = NULL, bidirection = NULL,vertex.size = NULL,
alpha.image = 0.15, point.size = 1.5,
group = NULL,cell.order = NULL,small.gap = 1, big.gap = 10, scale = FALSE, reduce = -1, show.legend = FALSE, legend.pos.x = 20, legend.pos.y = 20, nCol = NULL,
...) {
layout <- match.arg(layout)
# if (!is.null(vertex.size)) {
# warning("'vertex.size' is deprecated. Use `vertex.weight`")
# }
if (is.null(vertex.weight)) {
vertex.weight <- as.numeric(table(object@idents))
}
if (is.null(vertex.size.max)) {
if (length(unique(vertex.weight)) == 1) {
vertex.size.max <- 5
} else {
vertex.size.max <- 15
}
}
pairLR <- searchPair(signaling = signaling, pairLR.use = object@LR$LRsig, key = "pathway_name", matching.exact = T, pair.only = F)
if (is.null(signaling.name)) {
signaling.name <- signaling
}
net <- object@net
pairLR.use.name <- dimnames(net$prob)[[3]]
pairLR.name <- intersect(rownames(pairLR), pairLR.use.name)
if (!is.null(pairLR.use)) {
if (is.data.frame(pairLR.use)) {
pairLR.name <- intersect(pairLR.name, as.character(pairLR.use$interaction_name))
} else {
pairLR.name <- intersect(pairLR.name, as.character(pairLR.use))
}
if (length(pairLR.name) == 0) {
stop("There is no significant communication for the input L-R pairs!")
}
}
pairLR <- pairLR[pairLR.name, ]
prob <- net$prob
pval <- net$pval
prob[pval > thresh] <- 0
if (length(pairLR.name) > 1) {
pairLR.name.use <- pairLR.name[apply(prob[,,pairLR.name], 3, sum) != 0]
} else {
pairLR.name.use <- pairLR.name[sum(prob[,,pairLR.name]) != 0]
}
if (length(pairLR.name.use) == 0) {
stop(paste0('There is no significant communication of ', signaling.name))
} else {
pairLR <- pairLR[pairLR.name.use,]
}
nRow <- length(pairLR.name.use)
prob <- prob[,,pairLR.name.use]
pval <- pval[,,pairLR.name.use]
if (is.null(nCol)) {
nCol <- min(length(pairLR.name.use), 2)
}
if (length(dim(prob)) == 2) {
prob <- replicate(1, prob, simplify="array")
pval <- replicate(1, pval, simplify="array")
}
# prob <-(prob-min(prob))/(max(prob)-min(prob))
if (is.null(edge.weight.max)) {
edge.weight.max = max(prob)
}
if (layout == "hierarchy") {
if (graphics.init) {
par(mfrow=c(nRow,2), mar = c(5, 4, 4, 2) +0.1)
}
for (i in 1:length(pairLR.name.use)) {
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_hierarchy1(prob.i, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max, title.name = signalName_i,...)
netVisual_hierarchy2(prob.i, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max, title.name = signalName_i,...)
}
# grid.echo()
# gg <- grid.grab()
gg <- recordPlot()
} else if (layout == "circle") {
# par(mfrow=c(nRow,1))
if (graphics.init) {
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
}
gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
gg[[i]] <- netVisual_circle(prob.i, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
} else if (layout == "spatial") {
# par(mfrow=c(nRow,1))
if (graphics.init) {
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
}
coordinates <- object@images$coordinates
labels <- object@idents
meta.t <- object@meta
meta.t$labels <- labels
gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
gg[[i]] <- netVisual_spatial(prob.i, coordinates = coordinates, meta = meta.t, sample.use = sample.use, alpha.image = alpha.image, point.size = point.size, sources.use = sources.use, targets.use = targets.use, idents.use = idents.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max, edge.width.max=edge.width.max,title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
} else if (layout == "chord") {
if (graphics.init) {
par(mfrow = c(ceiling(length(pairLR.name.use)/nCol), nCol), xpd=TRUE)
}
gg <- vector("list", length(pairLR.name.use))
for (i in 1:length(pairLR.name.use)) {
title.name <- pairLR$interaction_name_2[i]
net <- prob[,,i]
gg[[i]] <- netVisual_chord_cell_internal(net, color.use = color.use, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate,
group = group, cell.order = cell.order,
lab.cex = vertex.label.cex,small.gap = small.gap, big.gap = big.gap,
scale = scale, reduce = reduce,
title.name = title.name, show.legend = show.legend, legend.pos.x = legend.pos.x, legend.pos.y = legend.pos.y)
}
}
return(gg)
}
#' Hierarchy plot of cell-cell communications sending to cell groups in vertex.receiver
#'
#' The width of edges represent the strength of the communication.
#'
#' @param net a weighted matrix defining the signaling network
#' @param vertex.receiver a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
#' @param color.use the character vector defining the color of each cell group
#' @param title.name alternative signaling pathway name to show on the plot
#' @param sources.use a vector giving the index or the name of source cell groups
#' @param targets.use a vector giving the index or the name of target cell groups.
#' @param remove.isolate whether remove the isolate nodes in the communication network
#' @param top the fraction of interactions to show
#' @param weight.scale whether rescale the edge weights
#' @param vertex.weight The weight of vertex: either a scale value or a vector
#' @param vertex.weight.max the maximum weight of vertex; defualt = max(vertex.weight)
#' @param vertex.size.max the maximum vertex size for visualization
#' @param edge.weight.max the maximum weight of edge; defualt = max(net)
#' @param edge.width.max The maximum edge width for visualization
#' @param label.dist the distance between labels and dot position
#' @param space.v the space between different columns in the plot
#' @param space.h the space between different rows in the plot
#' @param edge.curved Specifies whether to draw curved edges, or not.
#' This can be a logical or a numeric vector or scalar.
#' First the vector is replicated to have the same length as the number of
#' edges in the graph. Then it is interpreted for each edge separately.
#' A numeric value specifies the curvature of the edge; zero curvature means
#' straight edges, negative values means the edge bends clockwise, positive
#' values the opposite. TRUE means curvature 0.5, FALSE means curvature zero
#' @param shape The shape of the vertex, currently “circle”, “square”,
#' “csquare”, “rectangle”, “crectangle”, “vrectangle”, “pie” (see
#' vertex.shape.pie), ‘sphere’, and “none” are supported, and only by the
#' plot.igraph command. “none” does not draw the vertices at all, although
#' vertex label are plotted (if given). See shapes for details about vertex
#' shapes and vertex.shape.pie for using pie charts as vertices.
#' @param margin The amount of empty space below, over, at the left and right
#' of the plot, it is a numeric vector of length four. Usually values between
#' 0 and 0.5 are meaningful, but negative values are also possible, that will
#' make the plot zoom in to a part of the graph. If it is shorter than four
#' then it is recycled.
#' @param vertex.label.cex The label size of vertex
#' @param vertex.label.color The color of label for vertex
#' @param arrow.width The width of arrows
#' @param arrow.size the size of arrow
#' @param alpha.edge the transprency of edge
#' @param label.edge whether label edge
#' @param edge.label.color The color for single arrow
#' @param edge.label.cex The size of label for arrows
#' @param vertex.size Deprecated. Use `vertex.weight`
#' @importFrom igraph graph_from_adjacency_matrix ends E V layout_
#' @importFrom grDevices adjustcolor recordPlot
#' @importFrom shape Arrows
#' @return an object of class "recordedplot"
#' @export
netVisual_hierarchy1 <- function(net, vertex.receiver, color.use = NULL, title.name = NULL, sources.use = NULL, targets.use = NULL, remove.isolate = FALSE, top = 1,
weight.scale = FALSE, vertex.weight=20, vertex.weight.max = NULL, vertex.size.max = NULL,
edge.weight.max = NULL, edge.width.max=8, alpha.edge = 0.6,
label.dist = 2.8, space.v = 1.5, space.h = 1.6, shape= NULL, label.edge=FALSE,edge.curved=0, margin=0.2,
vertex.label.cex=0.6,vertex.label.color= "black",arrow.width=1,arrow.size = 0.2,edge.label.color='black',edge.label.cex=0.5, vertex.size = NULL){
if (!is.null(vertex.size)) {
warning("'vertex.size' is deprecated. Use `vertex.weight`")
}
if (is.null(vertex.size.max)) {
if (length(unique(vertex.weight)) == 1) {
vertex.size.max <- 5
} else {
vertex.size.max <- 15
}
}
options(warn = -1)
thresh <- stats::quantile(net, probs = 1-top)
net[net < thresh] <- 0
cells.level <- rownames(net)
if ((!is.null(sources.use)) | (!is.null(targets.use))) {
df.net <- reshape2::melt(net, value.name = "value")
colnames(df.net)[1:2] <- c("source","target")
# keep the interactions associated with sources and targets of interest
if (!is.null(sources.use)){
if (is.numeric(sources.use)) {
sources.use <- cells.level[sources.use]
}
df.net <- subset(df.net, source %in% sources.use)
}
if (!is.null(targets.use)){
if (is.numeric(targets.use)) {
targets.use <- cells.level[targets.use]
}
df.net <- subset(df.net, target %in% targets.use)
}
df.net$source <- factor(df.net$source, levels = cells.level)
df.net$target <- factor(df.net$target, levels = cells.level)
df.net$value[is.na(df.net$value)] <- 0
net <- tapply(df.net[["value"]], list(df.net[["source"]], df.net[["target"]]), sum)
}
net[is.na(net)] <- 0
if (remove.isolate) {
idx1 <- which(Matrix::rowSums(net) == 0)
idx2 <- which(Matrix::colSums(net) == 0)
idx <- intersect(idx1, idx2)
net <- net[-idx, ]
net <- net[, -idx]
}
if (is.null(color.use)) {
color.use <- scPalette(nrow(net))
}
if (is.null(vertex.weight.max)) {
vertex.weight.max <- max(vertex.weight)
}
vertex.weight <- vertex.weight/vertex.weight.max*vertex.size.max+6
m <- length(vertex.receiver)
net2 <- net
reorder.row <- c(vertex.receiver, setdiff(1:nrow(net),vertex.receiver))
net2 <- net2[reorder.row,vertex.receiver]
# Expand out to symmetric (M+N)x(M+N) matrix
m1 <- nrow(net2); n1 <- ncol(net2)
net3 <- rbind(cbind(matrix(0, m1, m1), net2), matrix(0, n1, m1+n1))
row.names(net3) <- c(row.names(net)[vertex.receiver], row.names(net)[setdiff(1:m1,vertex.receiver)], rep("",m))
colnames(net3) <- row.names(net3)
color.use3 <- c(color.use[vertex.receiver], color.use[setdiff(1:m1,vertex.receiver)], rep("#FFFFFF",length(vertex.receiver)))
color.use3.frame <- c(color.use[vertex.receiver], color.use[setdiff(1:m1,vertex.receiver)], color.use[vertex.receiver])
if (length(vertex.weight) != 1) {
vertex.weight = c(vertex.weight[vertex.receiver], vertex.weight[setdiff(1:m1,vertex.receiver)],vertex.weight[vertex.receiver])
}
if (is.null(shape)) {
shape <- c(rep("circle",m), rep("circle", m1-m), rep("circle",m))
}
g <- graph_from_adjacency_matrix(net3, mode = "directed", weighted = T)
edge.start <- ends(g, es=E(g), names=FALSE)
coords <- matrix(NA, nrow(net3), 2)
coords[1:m,1] <- 0; coords[(m+1):m1,1] <- space.h; coords[(m1+1):nrow(net3),1] <- space.h/2;
coords[1:m,2] <- seq(space.v, 0, by = -space.v/(m-1)); coords[(m+1):m1,2] <- seq(space.v, 0, by = -space.v/(m1-m-1));coords[(m1+1):nrow(net3),2] <- seq(space.v, 0, by = -space.v/(n1-1));
coords_scale<-coords
igraph::V(g)$size<-vertex.weight
igraph::V(g)$color<-color.use3[igraph::V(g)]
igraph::V(g)$frame.color <- color.use3.frame[igraph::V(g)]
igraph::V(g)$label.color <- vertex.label.color
igraph::V(g)$label.cex<-vertex.label.cex
if(label.edge){
E(g)$label<-E(g)$weight
igraph::E(g)$label <- round(igraph::E(g)$label, digits = 1)
}
if (is.null(edge.weight.max)) {
edge.weight.max <- max(igraph::E(g)$weight)
}
if (weight.scale == TRUE) {
# E(g)$width<-0.3+edge.max.width/(max(E(g)$weight)-min(E(g)$weight))*(E(g)$weight-min(E(g)$weight))
E(g)$width<- 0.3+E(g)$weight/edge.weight.max*edge.width.max
}else{
E(g)$width<-0.3+edge.width.max*E(g)$weight
}
E(g)$arrow.width<-arrow.width
E(g)$arrow.size<-arrow.size
E(g)$label.color<-edge.label.color
E(g)$label.cex<-edge.label.cex
E(g)$color<-adjustcolor(igraph::V(g)$color[edge.start[,1]],alpha.edge)
label.dist <- c(rep(space.h*label.dist,m), rep(space.h*label.dist, m1-m),rep(0, nrow(net3)-m1))
label.locs <- c(rep(-pi, m), rep(0, m1-m),rep(-pi, nrow(net3)-m1))
# text.pos <- cbind(c(-space.h/1.5, space.h/10, space.h/1.2), space.v-space.v/10)
text.pos <- cbind(c(-space.h/1.5, space.h/22, space.h/1.5), space.v-space.v/7)
igraph::add.vertex.shape("fcircle", clip=igraph::igraph.shape.noclip,plot=mycircle, parameters=list(vertex.frame.color=1, vertex.frame.width=1))
plot(g,edge.curved=edge.curved,layout=coords_scale,margin=margin,rescale=T,vertex.shape="fcircle", vertex.frame.width = c(rep(1,m1), rep(2,nrow(net3)-m1)),
vertex.label.degree=label.locs, vertex.label.dist=label.dist, vertex.label.family="Helvetica")
text(text.pos, c("Source","Target","Source"), cex = 0.8, col = c("#c51b7d","#c51b7d","#2f6661"))
arrow.pos1 <- c(-space.h/1.5, space.v-space.v/4, space.h/100000, space.v-space.v/4)
arrow.pos2 <- c(space.h/1.5, space.v-space.v/4, space.h/20, space.v-space.v/4)
shape::Arrows(arrow.pos1[1], arrow.pos1[2], arrow.pos1[3], arrow.pos1[4], col = "#c51b7d",arr.lwd = 0.0001,arr.length = 0.2, lwd = 0.8,arr.type="triangle")
shape::Arrows(arrow.pos2[1], arrow.pos2[2], arrow.pos2[3], arrow.pos2[4], col = "#2f6661",arr.lwd = 0.0001,arr.length = 0.2, lwd = 0.8,arr.type="triangle")
if (!is.null(title.name)) {
title.pos = c(space.h/8, space.v)
text(title.pos[1],title.pos[2],paste0(title.name, " signaling network"), cex = 1)
}
# https://www.andrewheiss.com/blog/2016/12/08/save-base-graphics-as-pseudo-objects-in-r/
# grid.echo()
# gg <- grid.grab()
gg <- recordPlot()
return(gg)
}