Cleaned up item clustering; works well now
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@ -10,13 +10,14 @@
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# input: results/haum/eventlogs_pre-corona_cleaned.RData
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# results/haum/pn_infos_items.csv
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# output: results/haum/eventlogs_pre-corona_item-clusters.csv
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# results/figures/clustering_artworks.pdf
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# results/figures/clustering_artworks.png
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#
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# last mod: 2024-03-06
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# last mod: 2024-03-08
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# setwd("C:/Users/nwickelmaier/Nextcloud/Documents/MDS/2023ss/60100_master_thesis/analysis/code")
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library(bupaverse)
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library(factoextra)
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source("R_helpers.R")
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#--------------- (1) Read data ---------------
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@ -31,17 +32,6 @@ datitem <- read.table("results/haum/pn_infos_items.csv", header = TRUE,
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#--------------- (1.3) Extract additional infos for clustering ---------------
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time_minmax_ms <- function(subdata) {
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subdata$min_time <- min(subdata$timeMs.start)
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if (all(is.na(subdata$timeMs.stop))) {
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subdata$max_time <- NA
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} else {
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subdata$max_time <- max(subdata$timeMs.stop, na.rm = TRUE)
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}
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subdata
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}
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# TODO: Move to helper file
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# Get average duration per path
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dat_split <- split(dat, ~ path)
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dat_list <- pbapply::pblapply(dat_split, time_minmax_ms)
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@ -63,11 +53,14 @@ datitem$nflipCard <- aggregate(event ~ item, dat, table)$event[,"flipCard"]
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datitem$nopenTopic <- aggregate(event ~ item, dat, table)$event[,"openTopic"]
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datitem$nopenPopup <- aggregate(event ~ item, dat, table)$event[,"openPopup"]
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rm(datpath)
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#--------------- (2) Clustering ---------------
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df <- datitem[, c("precision", "generalizability", "nvariants", "duration",
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"distance", "scaleSize", "rotationDegree", "npaths",
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"ncases", "nmoves", "nopenTopic", "nopenPopup")] |>
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"ncases", "nmoves", "nflipCard", "nopenTopic",
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"nopenPopup")] |>
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scale()
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dist_mat <- dist(df)
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@ -87,52 +80,54 @@ for (hc in hcs) plot(hc, main = "")
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hc <- hcs$ward
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k <- 4 # number of clusters
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factoextra::fviz_nbclust(df, FUNcluster = factoextra::hcut, method = "wss")
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factoextra::fviz_nbclust(df, FUNcluster = factoextra::hcut, method = "silhouette")
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mycols <- c("#78004B", "#FF6900", "#3CB4DC", "#91C86E")
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gap_stat <- cluster::clusGap(df, FUNcluster = factoextra::hcut,
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hc_func = "agnes", hc_method = "ward",
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K.max = 10)
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factoextra::fviz_gap_stat(gap_stat)
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grp <- cutree(hc, k = k)
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datitem$grp <- grp
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k <- 6 # number of clusters
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fviz_dend(hc, k = k,
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cex = 0.5,
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k_colors = mycols,
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#type = "phylogenic",
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rect = TRUE
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mycols <- c("#434F4F", "#78004B", "#FF6900", "#3CB4DC", "#91C86E", "Black")
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cluster <- cutree(hc, k = k)
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factoextra::fviz_dend(hc, k = k,
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cex = 0.5,
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k_colors = mycols,
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#type = "phylogenic",
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rect = TRUE
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)
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p <- fviz_cluster(list(data = df, cluster = grp),
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palette = mycols,
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ellipse.type = "convex",
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repel = TRUE,
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show.clust.cent = FALSE, ggtheme = theme_bw())
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p
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factoextra::fviz_cluster(list(data = df, cluster = cluster),
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palette = mycols,
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ellipse.type = "convex",
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repel = TRUE,
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show.clust.cent = FALSE,
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ggtheme = ggplot2::theme_bw())
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aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths,
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ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ grp,
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ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ cluster,
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datitem, mean)
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aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths,
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ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ grp,
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ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ cluster,
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datitem, max)
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item <- sprintf("%03d", as.numeric(gsub("item_([0-9]{3})", "\\1",
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row.names(datitem))))
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# Something like a scree plot (??)
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plot(rev(hc$height), type = "b", pch = 16, cex = .5)
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datitem$item <- sprintf("%03d",
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as.numeric(gsub("item_([0-9]{3})", "\\1", row.names(datitem))))
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res <- merge(dat, datitem[, c("item", "grp")], by = "item", all.x = TRUE)
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res <- merge(dat, data.frame(item, cluster), by = "item", all.x = TRUE)
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res <- res[order(res$fileId.start, res$date.start, res$timeMs.start), ]
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# Look at clusters
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par(mfrow = c(2,2))
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vioplot::vioplot(duration ~ grp, res)
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vioplot::vioplot(distance ~ grp, res)
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vioplot::vioplot(scaleSize ~ grp, res)
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vioplot::vioplot(rotationDegree ~ grp, res)
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vioplot::vioplot(duration ~ cluster, res)
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vioplot::vioplot(distance ~ cluster, res)
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vioplot::vioplot(scaleSize ~ cluster, res)
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vioplot::vioplot(rotationDegree ~ cluster, res)
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write.table(res,
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file = "results/haum/eventlogs_pre-corona_item-clusters.csv",
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@ -144,59 +139,60 @@ write.table(res,
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res$start <- res$date.start
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res$complete <- res$date.stop
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for (cluster in sort(unique(res$grp))) {
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for (clst in sort(unique(res$cluster))) {
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alog <- activitylog(res[res$grp == cluster, ],
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case_id = "path",
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activity_id = "event",
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resource_id = "item",
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timestamps = c("start", "complete"))
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alog <- bupaR::activitylog(res[res$cluster == clst, ],
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case_id = "path",
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activity_id = "event",
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resource_id = "item",
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timestamps = c("start", "complete"))
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dfg <- process_map(alog,
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type_nodes = frequency("relative", color_scale = "Greys"),
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sec_nodes = frequency("absolute"),
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type_edges = frequency("relative", color_edges = "#FF6900"),
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sec_edges = frequency("absolute"),
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rankdir = "LR",
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render = FALSE)
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export_map(dfg,
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file_name = paste0("results/processmaps/dfg_cluster", cluster, "_R.pdf"),
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file_type = "pdf",
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title = paste("DFG Cluster", cluster))
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dfg <- processmapR::process_map(alog,
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type_nodes = processmapR::frequency("relative", color_scale = "Greys"),
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sec_nodes = processmapR::frequency("absolute"),
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type_edges = processmapR::frequency("relative", color_edges = "#FF6900"),
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sec_edges = processmapR::frequency("absolute"),
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rankdir = "LR",
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render = FALSE)
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processmapR::export_map(dfg,
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file_name = paste0("results/processmaps/dfg_cluster", clst, "_R.pdf"),
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file_type = "pdf",
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title = paste("DFG Cluster", clst))
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}
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#--------------- (3) Visualization with pictures ---------------
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library(png)
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library(jpeg)
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library(grid)
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coor_2d <- cmdscale(dist_mat, k = 2)
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pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 10)
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#png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 10, res = 300)
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items <- sprintf("%03d", as.numeric(rownames(datitem)))
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#pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 10)
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png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 10, res = 300)
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par(mai = c(.4,.4,.1,.1), mgp = c(2.4, 1, 0))
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plot(y ~ x, p$data, type = "n", ylim = c(-3.5, 2.8), xlim = c(-5, 10),
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plot(coor_2d, type = "n", ylim = c(-3.7, 2.6), xlim = c(-5, 10.5),
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xlab = "", ylab = "")
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for (item in sprintf("%03d", as.numeric(rownames(p$data)))) {
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for (item in items) {
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if (item == "125") {
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pic <- readJPEG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
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pic <- jpeg::readJPEG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
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item, "/", item, ".jpg"))
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} else {
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pic <- readPNG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
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item, "/", item, ".png"))
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pic <- png::readPNG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
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item, "/", item, ".png"))
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}
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img <- as.raster(pic[,,1:3])
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x <- p$data$x[sprintf("%03d", as.numeric(rownames(p$data))) == item]
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y <- p$data$y[sprintf("%03d", as.numeric(rownames(p$data))) == item]
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x <- coor_2d[items == item, 1]
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y <- coor_2d[items == item, 2]
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points(x, y,
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col = mycols[p$data$cluster[sprintf("%03d", as.numeric(rownames(p$data))) == item]],
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col = mycols[cluster[items == item]],
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cex = 9,
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pch = 15)
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