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fix error in i_set_edge_attr(x, attr(value, name), color code consist… #686

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fix error in i_set_edge_attr(x, attr(value, name), color code consist… #686

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18 changes: 10 additions & 8 deletions R/visualization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1653,6 +1653,11 @@ netVisual_diffInteraction <- function(object, comparison = c(1,2), measure = c("
}
}
net <- net.diff
if(measure %in% c("count", "weight", "count.merged", "weight.merged")) {
if (is.null(color.use)) {
color.use <- scPalette(length(colnames(net.diff)))
}
}
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")
Expand Down Expand Up @@ -1683,6 +1688,7 @@ netVisual_diffInteraction <- function(object, comparison = c(1,2), measure = c("
idx <- intersect(idx1, idx2)
net <- net[-idx, ]
net <- net[, -idx]
color.use <-color.use[-idx]
}

net[abs(net) < stats::quantile(abs(net), probs = 1-top, na.rm= T)] <- 0
Expand All @@ -1695,15 +1701,15 @@ netVisual_diffInteraction <- function(object, comparison = c(1,2), measure = c("
}else{
coords_scale<-coords
}
if (is.null(color.use)) {
color.use = scPalette(length(igraph::V(g)))
}
if (is.null(vertex.weight.max)) {
vertex.weight.max <- max(vertex.weight)
}
vertex.weight <- vertex.weight/vertex.weight.max*vertex.size.max+5

loop.angle<-ifelse(coords_scale[igraph::V(g),1]>0,-atan(coords_scale[igraph::V(g),2]/coords_scale[igraph::V(g),1]),pi-atan(coords_scale[igraph::V(g),2]/coords_scale[igraph::V(g),1]))
if (sum(edge.start[, 2] == edge.start[, 1]) != 0) {
loop.angle[which(edge.start[,2]==edge.start[,1])] <- loop.angle[edge.start[which(edge.start[,2]==edge.start[,1]),1]]
}
igraph::V(g)$size<-vertex.weight
igraph::V(g)$color<-color.use[igraph::V(g)]
igraph::V(g)$frame.color <- color.use[igraph::V(g)]
Expand Down Expand Up @@ -1733,18 +1739,14 @@ netVisual_diffInteraction <- function(object, comparison = c(1,2), measure = c("
igraph::E(g)$width<-0.3+edge.width.max*igraph::E(g)$weight
}


if(sum(edge.start[,2]==edge.start[,1])!=0){
igraph::E(g)$loop.angle[which(edge.start[,2]==edge.start[,1])]<-loop.angle[edge.start[which(edge.start[,2]==edge.start[,1]),1]]
}
radian.rescale <- function(x, start=0, direction=1) {
c.rotate <- function(x) (x + start) %% (2 * pi) * direction
c.rotate(scales::rescale(x, c(0, 2 * pi), range(x)))
}
label.locs <- radian.rescale(x=1:length(igraph::V(g)), direction=-1, start=0)
label.dist <- vertex.weight/max(vertex.weight)+2
plot(g,edge.curved=edge.curved,vertex.shape=shape,layout=coords_scale,margin=margin, vertex.label.dist=label.dist,
vertex.label.degree=label.locs, vertex.label.family="Helvetica", edge.label.family="Helvetica") # "sans"
vertex.label.degree=label.locs, vertex.label.family="Helvetica", edge.label.family="Helvetica", edge.loop.angle=loop.angle) # "sans"
if (!is.null(title.name)) {
text(0,1.5,title.name, cex = 1.1)
}
Expand Down