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Last active November 24, 2016 19:50
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[メモ]有向グラフを活用して製造ラインの順序を可視化する ref: http://qiita.com/TomHortons/items/8bc0117bdeac4bb33e1c
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file0.txt
library(data.table)
library(dplyr)
#imports for plotting
require(GGally)
library(network)
library(sna)
library(ggplot2)
require(igraph)
require(intergraph)
library(stringr)
topFeaturesDate <- c("L3_S33_D3856","L3_S34_D3875","L3_S30_D3496","L3_S29_D3316","L3_S37_D3942",
"L3_S29_D3474","L0_S0_D1" , "L3_S30_D3506","L3_S30_D3501","L3_S30_D3726",
"L3_S30_D3566","L0_S3_D70" , "L3_S35_D3895","L0_S8_D145" , "L2_S26_D3037",
"L3_S35_D3886","L3_S35_D3900","L0_S13_D355" , "L3_S36_D3919","L0_S1_D26" ,
"L3_S36_D3928","L2_S26_D3081","L1_S24_D1511","L0_S12_D331" , "L1_S24_D1809",
"L0_S2_D34","L1_S24_D1536","L0_S14_D360" , "L1_S24_D1558","L0_S23_D617" ,
"L0_S6_D120","L1_S24_D1566","L1_S24_D1576","L0_S20_D462" , "L0_S4_D106" ,
"L0_S1_D30","L0_S19_D454", "L0_S7_D137","L0_S9_D152" , "L1_S24_D1826",
"L0_S16_D423","L0_S17_D432" , "L1_S24_D1568","L0_S5_D115" , "L1_S24_D1674",
"L1_S24_D1570","L0_S18_D437" ,"L0_S10_D216","L0_S9_D157" , "L1_S24_D1522",
"L0_S4_D111","L2_S27_D3130","L0_S11_D280" , "L0_S22_D543" , "L0_S9_D162" ,
"L0_S10_D221","L0_S15_D395", "L0_S9_D167" , "L1_S24_D1765","L3_S31_D3836",
"L0_S22_D548","L1_S24_D1583","L0_S21_D469", "L1_S24_D1770","L0_S10_D231" ,
"L0_S22_D553","L0_S21_D474" , "L1_S25_D1854","L3_S32_D3852",
"L3_S39_D3966","L0_S21_D484" , "L1_S25_D1867","L3_S44_D4101","L3_S40_D3981",
"L3_S38_D3953","L0_S22_D558" , "L1_S25_D2780","L3_S43_D4062","L3_S49_D4208",
"L2_S28_D3223","L1_S24_D1116","L1_S25_D2788","L3_S45_D4125","L3_S49_D4218",
"L3_S50_D4242","L3_S40_D3985","L1_S25_D2471","L1_S25_D2058","L1_S25_D1891",
"L1_S24_D677","L1_S24_D1135","L3_S43_D4082","L1_S25_D2792","L1_S25_D1883",
"L3_S41_D3997","L1_S25_D2098","L1_S25_D1887","L1_S25_D2754","L1_S25_D2138",
"L3_S51_D4255","L1_S24_D1155","L1_S25_D1980","L1_S25_D2790","L3_S47_D4140",
"L1_S25_D3011","L1_S25_D2240","L1_S25_D2230","L1_S25_D2798","L1_S25_D1902",
"L1_S24_D702","L1_S24_D697","L3_S48_D4194","L1_S25_D2996","L1_S24_D1413",
"L1_S24_D818","L1_S24_D1168","L1_S24_D1163","L1_S24_D1171","L1_S24_D804",
"L1_S24_D909","L1_S24_D801","L1_S25_D2801","L1_S24_D1018","L1_S25_D2206","L1_S25_D2505")
#one expansion option would be to select a time frame to visualized
dtNum <- fread("../input/train_numeric.csv", select = c("Id", "Response"))
dtDate <- fread("../input/train_date.csv",select = c("Id",topFeaturesDate))
#for each job identify which stations are passed through and for those store the minimum time
for (station in paste0("S",0:51))
{
cols = min(which((grepl(station,colnames(dtDate)))))
if(!cols==Inf){
dtDate[,paste0(station) := dtDate[,cols,with = FALSE]]
}
}
#limit data to only when passed through station X
dtStations = dtDate[,!grepl("L",colnames(dtDate)),with=F]
#melt data to go from wide to long format
#join with numeric to have Response
#remove NA entries - these are plentiful as after melting each station-job combination has its own row
melt(dtStations,id.vars=c("Id")) %>%
left_join(dtNum, by = "Id") %>%
filter(!is.na(value)) -> dtStationsMFiltered
dtStationsMFiltered %>%
group_by(variable) %>%
summarize(stationCount=n()) -> stationCount
stationCount = rbind(stationCount,data.frame(variable=c("result-0","result-1"),
stationCount=c(table(dtNum$Response)[1],
table(dtNum$Response)[2])))
colnames(stationCount) = c("Node","stationCount")
#sort entries by ascending time
dtStationsMFiltered %>%
arrange(value) -> dtStationsMFiltered
dtStationsMFiltered %>%
group_by(Id) %>%
mutate(nextStation = lead(variable)) -> edgelistsComplete
rm(dtStations)
rm(dtStationsMFiltered)
rm(dtNum)
invisible(gc())
edgelistsComplete %>%
group_by(Id) %>%
filter(!(variable %in% nextStation)) -> startingPoints
startingPoints %>%
mutate(nextStation = variable) -> startingPoints
startingPoints$variable = as.character(startingPoints$variable)
startingPoints$nextStation = as.character(startingPoints$nextStation)
startingPoints$variable = "start"
edgelistsComplete %>%
group_by(Id) %>%
filter(!(nextStation %in% variable)) -> endPoints
endPoints$variable = as.character(endPoints$variable)
endPoints$nextStation = paste0("result-",endPoints$Response)
edgelistsComplete$variable = as.character(edgelistsComplete$variable)
edgelistsComplete$nextStation = as.character(edgelistsComplete$nextStation)
edgelistsComplete %>% filter(nextStation!="NA") -> edgelistsComplete
dataPlot = rbind(startingPoints,edgelistsComplete,endPoints)
dataPlot$variable = as.factor(dataPlot$variable)
dataPlot$nextStation = as.factor(dataPlot$nextStation)
rm(endPoints)
rm(startingPoints)
invisible(gc())
dataPlot$edge = paste0(dataPlot$variable,"%",dataPlot$nextStation)
dataPlot %>%
group_by(edge) %>%
summarize(weight = n()) -> plotDataSummarized
plotDataSummarized %>%
mutate(Source = str_split_fixed(edge,"%",2)[,1],
Target = str_split_fixed(edge,"%",2)[,2]) %>%
select(-edge) -> plotDataSummarized
plotDataSummarized %>%
select(Source,Target,weight) -> plotDataSummarized
#for each row obtain the subsequent statoin
#create a station-line mapping lookup
LineStations = NULL
for (station in unique(plotDataSummarized$Source)){
if(station!="start")
{
x=paste0("_",station,"_")
y=head(colnames(dtDate)[which(grepl(x,colnames(dtDate)))],1)
y=strsplit(y,"_")[[1]][1]
LineStations = rbind(LineStations,data.frame(Node=station,Line=y))
}
}
LineStations = rbind(LineStations,data.frame(Node=c("result-1","result-0","start"),Line=c("Outcome","Outcome","START")))
rm(dtDate)
invisible()
#plotting format
options(repr.plot.width=15, repr.plot.height=5)
#create network from edgelist
plotDataSummarized$weight = plotDataSummarized$weight / 100000
ig = graph.data.frame(plotDataSummarized)
y = data.frame(Node=V(ig)$name)
y %>% left_join(LineStations,by="Node") -> y
ig %>% set_vertex_attr("line", value = as.character(y$Line)) -> ig
y %>% left_join(stationCount,by="Node") -> y
y[y$Node=="start",]$stationCount=1
ig %>% set_vertex_attr("count", value = y$stationCount) -> ig
nodeCoordinates=data.frame(label=c("start","S0","S1","S2","S3","S4","S5","S6",
"S7","S8","S9","S10","S11","S12","S13",
"S14","S15","S16","S17","S18","S19",
"S20","S21","S22","S23","S24","S25",
"S26","S27","S28","S29","S30","S31",
"S32","S33","S34","S35","S36","S37",
"S38","S39","S40","S41","S43",
"S44","S45","S47","S48","S49",
"S50","S51","result-0","result-1"),
x=c(0,
1,2,3,3,4,4,5,5,6,6.75,8,7.25,
1,2,3,3,4,4,5,5,6,6.75,8,7.25,
6,6,6.75,8,7.25,
9,10,11,11,11,12,12,13,14,15,
9,10,11,12,12,13,14,15,16,16,17,
18,18),
y=c(5,
9,9,10,8,10,8,10,8,9,10,9,8,
5,5,6,4,6,4,6,4,5,6,5,4,
2,0,2,1,0,
7,7,8,7,6,8,6,7,7,7,
3,3,3,4,2,3,3,3,4,2,3,
7,3))
#setup plot
network = ggnet2(ig)
netCoordinates = select(network$data,label)
netCoordinates = left_join(netCoordinates,nodeCoordinates,by = "label")
netCoordinates = as.matrix(select(netCoordinates,x,y))
network = ggnet2(ig,
alpha = .5,
size="count",
label = T,
color = "line",palette = "Set1",
mode = netCoordinates,
size.cut=5,
arrow.size = 20,
edge.alpha = 0.2, edge.size = "weight",
legend.position = "bottom")
network
#### Response 0
dataPlot %>%
filter(Response == 0) %>%
group_by(edge) %>%
summarize(weight = n()) -> plotDataSummarized
plotDataSummarized %>%
mutate(Source = str_split_fixed(edge,"%",2)[,1],
Target = str_split_fixed(edge,"%",2)[,2]) %>%
select(-edge) -> plotDataSummarized
plotDataSummarized %>%
select(Source,Target,weight) -> plotDataSummarized
#create network from edgelist
plotDataSummarized$weight = plotDataSummarized$weight /100000
ig = graph.data.frame(plotDataSummarized)
y = data.frame(Node=V(ig)$name)
y %>% left_join(LineStations,by="Node") -> y
ig %>% set_vertex_attr("line", value = as.character(y$Line)) -> ig
y %>% left_join(stationCount,by="Node") -> y
y[y$Node=="start",]$stationCount=1
ig %>% set_vertex_attr("count", value = y$stationCount) -> ig
#setup plot
network = ggnet2(ig)
netCoordinates = select(network$data,label)
netCoordinates = left_join(netCoordinates,nodeCoordinates,by = "label")
netCoordinates = as.matrix(select(netCoordinates,x,y))
network = ggnet2(ig,
alpha = .5,
size="count",
label = T,
color = "line",palette = "Set1",
mode = netCoordinates,
size.cut=5,
edge.alpha = 0.2, edge.size = "weight",
arrow.size = 20,
legend.position = "bottom")
network
##### Response 1
dataPlot %>%
filter(Response==1) %>%
group_by(edge) %>%
summarize(weight = n()) -> plotDataSummarized
plotDataSummarized %>%
mutate(Source = str_split_fixed(edge,"%",2)[,1],
Target = str_split_fixed(edge,"%",2)[,2]) %>%
select(-edge) -> plotDataSummarized
plotDataSummarized %>%
select(Source,Target,weight) -> plotDataSummarized
#create network from edgelist
plotDataSummarized$weight = plotDataSummarized$weight / 500
ig = graph.data.frame(plotDataSummarized)
y = data.frame(Node=V(ig)$name)
y %>% left_join(LineStations,by="Node") -> y
ig %>% set_vertex_attr("line", value = as.character(y$Line)) -> ig
y %>% left_join(stationCount,by="Node") -> y
y[y$Node=="start",]$stationCount=1
ig %>% set_vertex_attr("count", value = y$stationCount) -> ig
#setup plot
network = ggnet2(ig)
netCoordinates = select(network$data,label)
netCoordinates = left_join(netCoordinates,nodeCoordinates,by = "label")
netCoordinates = as.matrix(select(netCoordinates,x,y))
network = ggnet2(ig,
alpha = .5,
size="count",
label = T,
color = "line",palette = "Set1",
mode = netCoordinates,
size.cut=5,
edge.alpha = 0.2, edge.size = "weight",
arrow.size = 20,
legend.position = "bottom")
#output plot on graphics device
print(network)
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