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fixed plot script (nets)
1 parent 32b758d commit a263126

7 files changed

Lines changed: 55 additions & 41 deletions

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‎src/Labatut2022.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ data <- read.corpus.data()
6262
compute.static.statistics.base(data)
6363

6464
# plot these stats
65-
#generate.static.plots(data)
65+
generate.static.plots.base(data)
6666

6767

6868

‎src/common/file_system.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -206,13 +206,13 @@ get.path.stat.table <- function(object, mode, net.type, order=NA, window.size=NA
206206
if(!is.na(arc) && (!is.logical(arc) || arc))
207207
{ folder <- file.path(folder, "arcs")
208208
if(!is.logical(arc))
209-
folder <- file.path(folder, arc)
209+
folder <- file.path(folder, "separate", arc)
210210
}
211211
# possibly add volume subfolder
212212
if(!is.na(vol) && (!is.logical(vol) || vol))
213213
{ folder <- file.path(folder, "volumes")
214214
if(!is.logical(vol))
215-
folder <- file.path(folder, vol)
215+
folder <- file.path(folder, "separate", vol)
216216
}
217217
# possibly add window size
218218
if(!is.na(window.size))

‎src/measures/topological/degree.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -111,8 +111,8 @@ NODE_MEASURES[[paste0(MEAS_DEGREE,SFX_NORM)]] <- list( #degree-norm
111111
type=numeric(),
112112
bounds=c(0,1),
113113
cname="Normalized Degree",
114-
folder="nodes",
115-
object="graph",
114+
folder=MEAS_DEGREE,
115+
object="nodes",
116116
weighted=FALSE,
117117
foo=function(graph)
118118
{ compute.degree(paste0(MEAS_DEGREE,SFX_NORM), graph)

‎src/measures/topological/element.R‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@ GRAPH_MEASURES[[paste0(MEAS_NODE,SFX_NBR)]] <- list( #node-number
1111
cname="Node Number",
1212
folder="basic",
1313
object="graph",
14+
weighted=FALSE,
1415
foo=function(graph)
1516
{ vcount(graph=graph)
1617
}

‎src/post/description/deg_plots.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ for(meas in meass)
6767
data[[1]] <- tab[,meas]
6868
unfilt.idx <- data[[1]] > 0
6969
data[[1]] <- data[[1]][unfilt.idx] # remove isolates
70-
# file <- get.path.stats.comp(object="nodes", mode="scenes", meas.name=meas, weights=if(is.na(wt)) "none" else wt, filtered=FALSE, suf="disttest_noisolates")
70+
# file <- get.path.stats.comp(mode="scenes", meas.name=meas, weights=if(is.na(wt)) "none" else wt, filtered=FALSE, suf="distrtest_noisolates")
7171
# test.disc.distr(data[[1]], xlab=paste0("Unfiltered ",ALL_MEASURES[[meas]]$cname," (no isolates)"), return_stats=FALSE, sims=100, plot.file=file)
7272
# filtered
7373
file <- get.path.stat.table(object="nodes", mode="scenes", net.type="static", weights=if(is.na(wt)) "occurrences" else wt, filtered="filtered")
@@ -76,7 +76,7 @@ for(meas in meass)
7676
filt.idx <- data[[2]] > 1
7777
data[[2]] <- data[[2]][filt.idx] # remove isolates
7878
names(data) <- c("Unfiltered","Filtered")
79-
# file <- get.path.stats.comp(object="nodes", mode="scenes", meas.name=meas, weights=if(is.na(wt)) "none" else wt, filtered=TRUE, suf="disttest_noisolates")
79+
# file <- get.path.stats.comp(mode="scenes", meas.name=meas, weights=if(is.na(wt)) "none" else wt, filtered=TRUE, suf="distrtest_noisolates")
8080
# test.disc.distr(data[[2]], xlab=paste0("Unfiltered ",ALL_MEASURES[[meas]]$cname," (no isolates)"), return_stats=FALSE, sims=100, plot.file=file)
8181

8282
# set params

‎src/static/compute_stats.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -251,7 +251,7 @@ compute.static.nodecomp.statistics <- function(g, mode, window.size=NA, overlap=
251251
ylab <- "Frequency"
252252
}
253253

254-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, overlap=overlap, suf=paste0(md2,"_",md1,"_barplot"))
254+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, overlap=overlap, suf=paste0(md2,"_",md1,"_barplot"))
255255
for(fformat in PLOT_FORMAT)
256256
{ if(fformat==PLOT_FORMAT_PDF)
257257
pdf(file=paste0(plot.file,PLOT_FORMAT_PDF), bg="white")

‎src/static/plot_stats.R‎

Lines changed: 46 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -297,7 +297,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
297297
names(values) <- nms
298298

299299
# generate the boxplot plot
300-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, suf="boxplot")
300+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, suf="boxplot")
301301
tlog(5,"Plotting file \"",plot.file,"\"")
302302
for(fformat in PLOT_FORMAT)
303303
{ if(fformat==PLOT_FORMAT_PDF)
@@ -322,7 +322,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
322322
}
323323

324324
# generate the violin plot
325-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, suf="violin")
325+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, suf="violin")
326326
tlog(5,"Plotting file \"",plot.file,"\"")
327327
for(fformat in PLOT_FORMAT)
328328
{ if(fformat==PLOT_FORMAT_PDF)
@@ -347,7 +347,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
347347
}
348348

349349
# generate distribution plots
350-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, suf="distrib")
350+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, suf="distrib")
351351
tlog(5,"Plotting file \"",plot.file,"\"")
352352
cols <- c("BLACK", "BLACK", viridis(length(values)-2))
353353
lty <- c(2, 3, rep(1,length(values)-1))
@@ -391,7 +391,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
391391
names(values) <- nms
392392

393393
# generate the boxplot
394-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap=overlap, suf="boxplot")
394+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap=overlap, suf="boxplot")
395395
tlog(5,"Plotting file \"",plot.file,"\"")
396396
for(fformat in PLOT_FORMAT)
397397
{ if(fformat==PLOT_FORMAT_PDF)
@@ -416,7 +416,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
416416
}
417417

418418
# generate the violin plot
419-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap=overlap, suf="violin")
419+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap=overlap, suf="violin")
420420
tlog(5,"Plotting file \"",plot.file,"\"")
421421
for(fformat in PLOT_FORMAT)
422422
{ if(fformat==PLOT_FORMAT_PDF)
@@ -436,7 +436,7 @@ generate.static.plots.single <- function(mode, window.sizes, overlaps)
436436
}
437437

438438
# generate distribution plots
439-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap=overlap, suf="distrib")
439+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap=overlap, suf="distrib")
440440
tlog(5,"Plotting file \"",plot.file,"\"")
441441
cols <- c("BLACK", "BLACK", viridis(length(values)-2))
442442
lty <- c(2, 3, rep(1,length(values)-1))
@@ -517,7 +517,7 @@ generate.static.plots.multiple <- function(mode, window.sizes, overlaps)
517517
# generate a plot containing each window size value as a series
518518
#cols <- get.palette(length(data))
519519
cols <- viridis(length(data))
520-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size="", suf="series")
520+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size="", suf="series")
521521
tlog(5,"Plotting file \"",plot.file,"\"")
522522
if(all(is.na(unlist(data))))
523523
{ msg <- paste0("WARNING: All values are NA for ", plot.file)
@@ -587,7 +587,7 @@ generate.static.plots.multiple <- function(mode, window.sizes, overlaps)
587587
# generate a plot representing each overlap value as a series
588588
#cols <- get.palette(length(data))
589589
cols <- viridis(length(data))
590-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap="", suf="series")
590+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap="", suf="series")
591591
tlog(5,"Plotting file \"",plot.file,"\"")
592592
if(all(is.na(unlist(data))))
593593
{ msg <- paste0("WARNING: All values are NA for ", plot.file)
@@ -687,7 +687,7 @@ generate.static.plots.corr <- function(mode, window.sizes, overlaps)
687687
}
688688
# generate a plot containing each window size value as a series
689689
cols <- get.palette(length(data))
690-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size="", suf="corr")
690+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size="", suf="corr")
691691
tlog(5,"Plotting file \"",plot.file,"\"")
692692
if(all(is.na(unlist(data))))
693693
{ msg <- paste0("WARNING: All values are NA for ", plot.file)
@@ -748,7 +748,7 @@ generate.static.plots.corr <- function(mode, window.sizes, overlaps)
748748
}
749749
# generate a plot representing each overlap value as a series
750750
cols <- get.palette(length(data))
751-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap="", suf="corr")
751+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap="", suf="corr")
752752
tlog(5,"Plotting file \"",plot.file,"\"")
753753
if(all(is.na(unlist(data))))
754754
{ msg <- paste0("WARNING: All values are NA for ", plot.file)
@@ -804,7 +804,7 @@ generate.static.plots.corr <- function(mode, window.sizes, overlaps)
804804

805805
#############################################################################################
806806
# Generates a bar plot comparing two node or node-pair measures. The reference measure is used as
807-
# a baseline, and to order the nodes on the x axis. The comparison measure is used to process
807+
# a baseline, and to order the nodes on the x-axis. The comparison measure is used to process
808808
# the ranking difference with the reference measure, and the result appears as the bar heights.
809809
#
810810
# mode: either "panel.window" or "page.window" (not "scenes").
@@ -865,7 +865,7 @@ generate.static.plots.ranks <- function(mode, window.sizes, overlaps)
865865
colors <- heat.colors(max(ranks))
866866

867867
# generate the plot
868-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, overlap=overlap, suf=paste0("ranks=",substr(weights,1,3)))
868+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, overlap=overlap, suf=paste0("ranks=",substr(weights,1,3)))
869869
tlog(5,"Plotting file \"",plot.file,"\"")
870870
for(fformat in PLOT_FORMAT)
871871
{ if(fformat==PLOT_FORMAT_PDF)
@@ -960,7 +960,7 @@ generate.static.plots.tfpn <- function(mode, window.sizes=NA, overlaps=NA)
960960
ylab <- "Frequency"
961961
}
962962

963-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, window.size=window.size, suf=paste0(md,"_barplot"))
963+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, window.size=window.size, suf=paste0(md,"_barplot"))
964964
for(fformat in PLOT_FORMAT)
965965
{ if(fformat==PLOT_FORMAT_PDF)
966966
pdf(file=paste0(plot.file,PLOT_FORMAT_PDF), bg="white")
@@ -1007,7 +1007,7 @@ generate.static.plots.tfpn <- function(mode, window.sizes=NA, overlaps=NA)
10071007
ylab <- "Frequency"
10081008
}
10091009

1010-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, overlap=overlap, suf=paste0(md,"_barplot"))
1010+
plot.file <- get.path.stats.comp(mode=mode, meas.name=meas.name, overlap=overlap, suf=paste0(md,"_barplot"))
10111011
for(fformat in PLOT_FORMAT)
10121012
{ if(fformat==PLOT_FORMAT_PDF)
10131013
pdf(file=paste0(plot.file,PLOT_FORMAT_PDF), bg="white")
@@ -1071,11 +1071,16 @@ generate.static.plots.all <- function(mode, window.sizes, overlaps)
10711071
# filtered: whether to use the filtered version of the graph.
10721072
###############################################################################
10731073
generate.static.plots.scene <- function(arc=NA, vol=NA, filtered=FALSE)
1074-
{ filt.txt <- if(filtered) "filtered" else "unfiltered"
1074+
{ if(filtered)
1075+
{ col <- ATT_COLORS_FILT["Keep"]
1076+
filt.txt <- "filtered"
1077+
}
1078+
else
1079+
{ col <- ATT_COLORS_FILT["Discard"]
1080+
filt.txt <- "unfiltered"
1081+
}
10751082
tlog(3,"Generating plots for the ",filt.txt," scene-based graphs")
10761083
mode <- "scenes"
1077-
wmodes <- c("occurrences","duration")
1078-
col <- ATT_COLORS_FILT[if(filtered) "Keep" else "Discard"]
10791084

10801085
# list measures to plot
10811086
nmn <- names(NODE_MEASURES)
@@ -1093,6 +1098,11 @@ generate.static.plots.scene <- function(arc=NA, vol=NA, filtered=FALSE)
10931098
else if(meas.name %in% npmn)
10941099
object <- "nodepairs"
10951100

1101+
if(ALL_MEASURES[[meas.name]]$weighted)
1102+
wmodes <- c("occurrences","duration")
1103+
else
1104+
wmodes <- c("none")
1105+
10961106
# process each type of weight
10971107
for(wmode in wmodes)
10981108
{ tlog(4,"Dealing with weights=",wmode)
@@ -1104,8 +1114,7 @@ generate.static.plots.scene <- function(arc=NA, vol=NA, filtered=FALSE)
11041114
#vals <- vals[vals>0] # remove the zeroes?
11051115

11061116
# plot histogram
1107-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filtered, suf="histo")
1108-
# TODO why is this the "comparison" folder? shouldn't it be stats or plots?
1117+
plot.file <- get.path.stats.topo(mode=mode, net.type="static", meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="histo")
11091118
for(fformat in PLOT_FORMAT)
11101119
{ if(fformat==PLOT_FORMAT_PDF)
11111120
pdf(file=paste0(plot.file,PLOT_FORMAT_PDF), bg="white")
@@ -1126,19 +1135,19 @@ generate.static.plots.scene <- function(arc=NA, vol=NA, filtered=FALSE)
11261135
}
11271136

11281137
# plot complementary cumulative distribution function
1129-
plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filtered, suf="ccdf")
1138+
plot.file <- get.path.stats.topo(mode=mode, net.type="static", meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="ccdf")
11301139
for(fformat in PLOT_FORMAT)
11311140
{ if(fformat==PLOT_FORMAT_PDF)
11321141
pdf(file=paste0(plot.file,PLOT_FORMAT_PDF), bg="white")
11331142
else if(fformat==PLOT_FORMAT_PNG)
11341143
png(filename=paste0(plot.file,PLOT_FORMAT_PNG), width=800, height=800, units="px", pointsize=20, bg="white")
1135-
plot.ccdf(data=vals, main=ml, xlab=xl, ylab="default", log=TRUE)
1144+
plot.ccdf(data=vals, main=ml, xlab=xl, ylab="default", cols=col, log=TRUE)
11361145
dev.off()
11371146
}
11381147

11391148
# test the type of distribution (very slow, doing it only for the whole graph)
11401149
if(is.na(arc) && is.na(vol))
1141-
{ plot.file <- get.path.stats.comp(object=object, mode=mode, meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filtered, suf="disttest")
1150+
{ plot.file <- get.path.stats.topo(mode=mode, net.type="static", meas.name=meas.name, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="distrtest")
11421151
if(all(vals%%1==0))
11431152
test.disc.distr(data=vals, xlab=ALL_MEASURES[[meas.name]]$cname, return_stats=TRUE, sims=100, plot.file=plot.file)
11441153
else
@@ -1157,32 +1166,32 @@ generate.static.plots.scene <- function(arc=NA, vol=NA, filtered=FALSE)
11571166
g.occ <- g; E(g.occ)$weight <- E(g)$Occurrences
11581167

11591168
# degree vs. neighbors' degree
1160-
filename <- get.path.stats.comp(object="nodes", mode="scenes", meas.name=MEAS_DEGREE, arc=arc, vol=vol, filtered=filtered)
1169+
filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_DEGREE, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="nei.deg_vs_degree")
11611170
neigh.degree.vs.degree(g, weights=FALSE, filename, col)
1162-
for(wmode in wmodes)
1163-
{ filename <- get.path.stats.comp(object="nodes", mode="scenes", meas.name="strength", weights=wmode, arc=arc, vol=vol, filtered=filtered)
1171+
for(wmode in c("occurrences","duration"))
1172+
{ filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_STRENGTH, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="nei.str_vs_strength")
11641173
if(wmode=="duration")
11651174
neigh.degree.vs.degree(g.dur, weights=TRUE, filename, col)
11661175
else if(wmode=="occurrences")
11671176
neigh.degree.vs.degree(g.occ, weights=TRUE, filename, col)
11681177
}
11691178

11701179
# degree vs. transitivity
1171-
filename <- get.path.stats.comp(object="nodes", mode="scenes", meas.name=MEAS_DEGREE, arc=arc, vol=vol, filtered=filtered)
1180+
filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_MULTI_NODES, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="transitivity_vs_degree")
11721181
transitivity.vs.degree(g, weights=FALSE, filename, col)
1173-
for(wmode in wmodes)
1174-
{ filename <- get.path.stats.comp(object="nodes", mode="scenes", meas.name="strength", weights=wmode, arc=arc, vol=vol, filtered=filtered)
1182+
for(wmode in c("occurrences","duration"))
1183+
{ filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_MULTI_NODES, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="transitivity_vs_strength")
11751184
if(wmode=="duration")
11761185
transitivity.vs.degree(g.dur, weights=TRUE, filename, col)
11771186
else if(wmode=="occurrences")
11781187
transitivity.vs.degree(g.occ, weights=TRUE, filename, col)
11791188
}
11801189

11811190
# hop plots
1182-
filename <- get.path.stats.comp(object="nodepairs", mode="scenes", meas.name=MEAS_DISTANCE, arc=arc, vol=vol, filtered=filtered)
1191+
filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_DISTANCE, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="hop-plot")
11831192
hop.plot(g, weights=FALSE, filename, col)
1184-
for(wmode in wmodes)
1185-
{ filename <- get.path.stats.comp(object="nodepairs", mode="scenes", meas.name="distance", weights=wmode, arc=arc, vol=vol, filtered=filtered)
1193+
for(wmode in c("occurrences","duration"))
1194+
{ filename <- get.path.stats.topo(mode=mode, net.type="static", meas.name=MEAS_DISTANCE, weights=wmode, arc=arc, vol=vol, filtered=filt.txt, suf="hop-plot")
11861195
if(wmode=="duration")
11871196
hop.plot(g.dur, weights=TRUE, filename, col)
11881197
else if(wmode=="occurrences")
@@ -1209,13 +1218,12 @@ generate.static.plots.evol <- function(data, arcs, filtered)
12091218
}
12101219
else
12111220
{ emode <- "volume"
1212-
items <- data$volume.stats[,COL_VOLUME]
1221+
items <- paste(1:nrow(data$volume.stats),"_",data$volume.stats[,COL_VOLUME],sep="")
12131222
}
12141223

12151224
# init other variables
12161225
tlog(3,"Generating ",emode,"-based evolution plots for the ",filt.txt," scene-based graphs")
12171226
mode <- "scenes"
1218-
wmodes <- c("occurrences","duration")
12191227
col <- ATT_COLORS_FILT[if(filtered) "Keep" else "Discard"]
12201228

12211229
# list measures to plot
@@ -1226,6 +1234,11 @@ generate.static.plots.evol <- function(data, arcs, filtered)
12261234
{ tlog(4,"Generating ",emode,"-based evolution plots for measure ",meas.name)
12271235
object <- "graph"
12281236

1237+
if(ALL_MEASURES[[meas.name]]$weighted)
1238+
wmodes <- c("occurrences","duration")
1239+
else
1240+
wmodes <- c("none")
1241+
12291242
# process each type of weight
12301243
for(wmode in wmodes)
12311244
{ tlog(4,"Dealing with weights=",wmode)

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