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marcoabreu pushed a commit to branch v1.0.0
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The following commit(s) were added to refs/heads/v1.0.0 by this push:
new 3df9bf8 R graph.viz fix (#10023)
3df9bf8 is described below
commit 3df9bf802021d5aa67c609c6736acee94aaf3a48
Author: jeremiedb <jeremi...@users.noreply.github.com>
AuthorDate: Wed Mar 7 08:28:23 2018 -0500
R graph.viz fix (#10023)
* R graph.viz fix
* sub
---
R-package/R/viz.graph.R | 129 ++++++++++++++++++++++++------------------------
1 file changed, 64 insertions(+), 65 deletions(-)
diff --git a/R-package/R/viz.graph.R b/R-package/R/viz.graph.R
index 6d13de0..abc8323 100644
--- a/R-package/R/viz.graph.R
+++ b/R-package/R/viz.graph.R
@@ -8,7 +8,6 @@
#' @importFrom stringr str_trim
#' @importFrom jsonlite fromJSON
#' @importFrom DiagrammeR create_graph
-#' @importFrom DiagrammeR set_global_graph_attrs
#' @importFrom DiagrammeR add_global_graph_attrs
#' @importFrom DiagrammeR create_node_df
#' @importFrom DiagrammeR create_edge_df
@@ -63,91 +62,91 @@ graph.viz <- function(symbol, shape=NULL, direction="TD",
type="graph", graph.wi
)
}
- model_list<- fromJSON(symbol$as.json())
- model_nodes<- model_list$nodes
- model_nodes$id<- 1:nrow(model_nodes)-1
- model_nodes$level<- model_nodes$ID
+ model_list <- fromJSON(symbol$as.json())
+ model_nodes <- model_list$nodes
+ model_nodes$id <- seq_len(nrow(model_nodes))-1
+ model_nodes$level <- model_nodes$ID
# extract IDs from string list
- tuple_str <- function(str) sapply(str_extract_all(str, "\\d+"), function(x)
paste0(x, collapse="X"))
+ tuple_str <- function(str) vapply(str_extract_all(str, "\\d+"),
+ function(x) paste0(x, collapse="X"),
+ character(1))
### substitute op for heads
- op_id<- sort(unique(model_list$heads[1,]+1))
- op_null<- which(model_nodes$op=="null")
- op_substitute<- intersect(op_id, op_null)
- model_nodes$op[op_substitute]<- model_nodes$name[op_substitute]
-
- model_nodes$color<- apply(model_nodes["op"], 1, get.color)
- model_nodes$shape<- apply(model_nodes["op"], 1, get.shape)
-
- label_paste <- paste0(
- model_nodes$op,
- "\n",
- model_nodes$name,
- "\n",
- model_nodes$attr$num_hidden %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
- model_nodes$attr$act_type %>% str_replace_na() %>% str_replace_all(pattern
= "NA", ""),
- model_nodes$attr$pool_type %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
- model_nodes$attr$kernel %>% tuple_str %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
- " / ",
- model_nodes$attr$stride %>% tuple_str %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
- ", ",
- model_nodes$attr$num_filter %>% str_replace_na() %>%
str_replace_all(pattern = "NA", "")
- ) %>%
+ op_id <- sort(unique(model_list$heads[1,]+1))
+ op_null <- which(model_nodes$op=="null")
+ op_substitute <- intersect(op_id, op_null)
+ model_nodes$op[op_substitute] <- model_nodes$name[op_substitute]
+
+ model_nodes$color <- apply(model_nodes["op"], 1, get.color)
+ model_nodes$shape <- apply(model_nodes["op"], 1, get.shape)
+
+ label_paste <- paste0(model_nodes$op,
+ "\n",
+ model_nodes$name,
+ "\n",
+ model_nodes$attr$num_hidden %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
+ model_nodes$attr$act_type %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
+ model_nodes$attr$pool_type %>% str_replace_na() %>%
str_replace_all(pattern = "NA", ""),
+ model_nodes$attr$kernel %>% tuple_str %>%
str_replace_na() %>% str_replace_all(pattern = "NA", ""),
+ " / ",
+ model_nodes$attr$stride %>% tuple_str %>%
str_replace_na() %>% str_replace_all(pattern = "NA", ""),
+ ", ",
+ model_nodes$attr$num_filter %>% str_replace_na() %>%
str_replace_all(pattern = "NA", "")) %>%
str_replace_all(pattern = "[^[:alnum:]]+$", "") %>%
str_trim
- model_nodes$label<- label_paste
+ model_nodes$label <- label_paste
id.to.keep <- model_nodes$id[!model_nodes$op=="null"]
nodes_df <- model_nodes[model_nodes$id %in% id.to.keep, c("id", "label",
"shape", "color")]
### remapping for DiagrammeR convention
- nodes_df$id<- nodes_df$id
- nodes_df$id_graph<- 1:nrow(nodes_df)
- id_dic<- nodes_df$id_graph
- names(id_dic)<- as.character(nodes_df$id)
-
- edges_id<- model_nodes$id[!sapply(model_nodes$inputs, length)==0 &
!model_nodes$op=="null"]
- edges_id<- id_dic[as.character(edges_id)]
- edges<- model_nodes$inputs[!sapply(model_nodes$inputs, length)==0 &
!model_nodes$op=="null"]
- edges<- sapply(edges, function(x)intersect(as.numeric(x[, 1]), id.to.keep),
simplify = F)
- names(edges)<- edges_id
-
- edges_df<- data.frame(
- from=unlist(edges),
- to=rep(names(edges), time=sapply(edges, length)),
- arrows = "to",
- color="black",
- from_name_output=paste0(model_nodes$name[unlist(edges)+1], "_output"),
- stringsAsFactors=F)
- edges_df$from<- id_dic[as.character(edges_df$from)]
-
- nodes_df_new<- create_node_df(n = nrow(nodes_df), label=nodes_df$label,
shape=nodes_df$shape, type="base", penwidth=2, color=nodes_df$color,
style="filled",
- fillcolor=adjustcolor(nodes_df$color, alpha.f
= 1), fontcolor = "black")
- edge_df_new<- create_edge_df(from = edges_df$from, to=edges_df$to,
color="black", fontcolor = "black")
-
- if (!is.null(shape)){
+ nodes_df$id <- nodes_df$id
+ nodes_df$id_graph <- seq_len(nrow(nodes_df))
+ id_dic <- nodes_df$id_graph
+ names(id_dic) <- as.character(nodes_df$id)
+
+ edges_id <- model_nodes$id[lengths(model_nodes$inputs)!=0 &
model_nodes$op!="null"]
+ edges_id <- id_dic[as.character(edges_id)]
+ edges <- model_nodes$inputs[lengths(model_nodes$inputs)!=0 &
model_nodes$op!="null"]
+ edges <- sapply(edges, function(x)intersect(as.numeric(x[, 1]), id.to.keep),
simplify = FALSE)
+ names(edges) <- edges_id
+
+ edges_df <- data.frame(from=unlist(edges),
+ to=rep(names(edges), time=lengths(edges)),
+ arrows = "to",
+ color="black",
+
from_name_output=paste0(model_nodes$name[unlist(edges)+1], "_output"),
+ stringsAsFactors=FALSE)
+ edges_df$from <- id_dic[as.character(edges_df$from)]
+
+ nodes_df_new <- create_node_df(n = nrow(nodes_df), label=nodes_df$label,
shape=nodes_df$shape, type="base", penwidth=2, color=nodes_df$color,
style="filled",
+ fillcolor=adjustcolor(nodes_df$color, alpha.f
= 1), fontcolor = "black")
+ edge_df_new <- create_edge_df(from = edges_df$from, to=edges_df$to,
color="black", fontcolor = "black")
+
+ if (!is.null(shape)) {
if (is.list(shape)) {
- edges_labels_raw<- symbol$get.internals()$infer.shape(shape)$out.shapes
- } else edges_labels_raw<-
symbol$get.internals()$infer.shape(list(data=shape))$out.shapes
- if (!is.null(edges_labels_raw)){
+ edges_labels_raw <- symbol$get.internals()$infer.shape(shape)$out.shapes
+ } else edges_labels_raw <-
symbol$get.internals()$infer.shape(list(data=shape))$out.shapes
+ if (!is.null(edges_labels_raw)) {
edge_label_str <- function(x) paste0(x, collapse="X")
- edges_labels_raw<- sapply(edges_labels_raw, edge_label_str)
- names(edges_labels_raw)[names(edges_labels_raw)=="data"]<- "data_output"
- edge_df_new$label<- edges_labels_raw[edges_df$from_name_output]
- edge_df_new$rel<- edge_df_new$label
+ edges_labels_raw <- vapply(edges_labels_raw, edge_label_str,
character(1))
+ names(edges_labels_raw)[names(edges_labels_raw)=="data"] <- "data_output"
+ edge_df_new$label <- edges_labels_raw[edges_df$from_name_output]
+ edge_df_new$rel <- edge_df_new$label
}
}
- graph<- create_graph(nodes_df = nodes_df_new, edges_df = edge_df_new,
directed = T) %>%
- set_global_graph_attrs("layout", value = "dot", attr_type = "graph") %>%
+ graph <- create_graph(nodes_df = nodes_df_new, edges_df = edge_df_new,
directed = TRUE, attr_theme = NULL) %>%
+ add_global_graph_attrs("layout", value = "dot", attr_type = "graph") %>%
add_global_graph_attrs("rankdir", value = direction, attr_type = "graph")
if (type=="vis"){
- graph_render<- render_graph(graph = graph, output = "visNetwork", width =
graph.width.px, height = graph.height.px) %>% visHierarchicalLayout(direction =
direction, sortMethod = "directed")
+ graph_render <- render_graph(graph = graph, output = "visNetwork", width =
graph.width.px, height = graph.height.px) %>%
+ visHierarchicalLayout(direction = direction, sortMethod = "directed")
} else {
- graph_render<- render_graph(graph = graph, output = "graph", width =
graph.width.px, height = graph.height.px)
+ graph_render <- render_graph(graph = graph, output = "graph", width =
graph.width.px, height = graph.height.px)
}
return(graph_render)
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