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netVisual functions need to pass object to netVisual_hierarchy2() #685

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netVisual functions need to pass object to netVisual_hierarchy2() #685

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18 changes: 9 additions & 9 deletions R/visualization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL
signalName_i <- pairLR$interaction_name_2[i]
prob.i <- prob[,,i]
netVisual_hierarchy1(prob.i, vertex.receiver = vertex.receiver, sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.i, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
netVisual_hierarchy2(prob.i, object, vertex.receiver = setdiff(1:nrow(prob.i),vertex.receiver), sources.use = sources.use, targets.use = targets.use, remove.isolate = remove.isolate, top = top, color.use = color.use, vertex.weight = vertex.weight, vertex.weight.max = vertex.weight.max, vertex.size.max = vertex.size.max, weight.scale = weight.scale, edge.weight.max = edge.weight.max.individual, edge.width.max=edge.width.max, title.name = signalName_i, vertex.label.cex = vertex.label.cex,...)
}
dev.off()
}
Expand All @@ -203,7 +203,7 @@ netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL
signalName_i <- pairLR$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,...)
netVisual_hierarchy2(prob.i, object, 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()
}
Expand All @@ -215,7 +215,7 @@ netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL
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,...)
netVisual_hierarchy2(prob.i, object, 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()
}
Expand All @@ -225,15 +225,15 @@ netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL
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,...)
netVisual_hierarchy2(prob.sum, object, 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,...)
netVisual_hierarchy2(prob.sum, object, 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()
}
Expand All @@ -242,7 +242,7 @@ netVisual <- function(object, signaling, signaling.name = NULL, color.use = NULL
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,...)
netVisual_hierarchy2(prob.sum, object, 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()
}
Expand Down Expand Up @@ -566,7 +566,7 @@ netVisual_aggregate <- function(object, signaling, signaling.name = NULL, color.
}
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,...)
netVisual_hierarchy2(prob.sum, object, 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()
Expand Down Expand Up @@ -752,7 +752,7 @@ netVisual_individual <- function(object, signaling, signaling.name = NULL, pairL
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,...)
netVisual_hierarchy2(prob.i, object, 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()
Expand Down Expand Up @@ -1046,7 +1046,7 @@ netVisual_hierarchy1 <- function(net, vertex.receiver, color.use = NULL, title.n
#' @importFrom shape Arrows
#' @return an object of class "recordedplot"
#' @export
netVisual_hierarchy2 <-function(net, vertex.receiver, color.use = NULL, title.name = NULL, sources.use = NULL, targets.use = NULL, remove.isolate = FALSE, top = 1,
netVisual_hierarchy2 <-function(net, object, 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,
Expand Down