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Update old version to new layout with added functionalities #2

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Merged
Mell-A merged 9 commits into from
Jun 13, 2025
Merged

Update old version to new layout with added functionalities #2

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3fe609e
Add pipeline
albamerdani Apr 3, 2025
c94c3b6
Included layout changes
hfri Apr 12, 2025
170e311
tree starts at fauna level; website still does not work
hfri Apr 19, 2025
502130f
added percentage
hfri May 3, 2025
e2daec1
put parts of the menu to the right of the plot
hfri May 11, 2025
1d85f8b
bug fix, tried to include download button -- still need to make it fu…
hfri May 16, 2025
952c4eb
Layout update and download option
hfri May 29, 2025
98b270f
small layout adaptions
hfri May 30, 2025
aed9a1f
solve merge conflict with main
hfri Jun 13, 2025
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247 changes: 0 additions & 247 deletions activity_heatmap.R
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72 changes: 3 additions & 69 deletions functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,11 @@ build_tree_from_concepts <- function(concepts, counts) {
for (i in 1:length(concepts)) {
dfn <- rbind(dfn, c(concepts[[i]]$id, concepts[[i]]$parent, concepts[[i]]$label))
}

names(dfn) <- c("from", "to", "label")
# filter concepts to only the base ontology
dfn <- dfn %>% filter(grepl("SCCSSOntology", from))

tree <- FromDataFrameNetwork(dfn, check = "check")
trav <- Traverse(tree)
trav_name <- Get(trav, "name")
Expand All @@ -80,7 +81,7 @@ build_tree_from_concepts <- function(concepts, counts) {
df_counts <- bind_rows(dfs)
# order df according to traverse sequence
f <- df_counts[match(trav_name, df_counts$X_value), "frequency"]

# set new attribute
tree$Set(freq = f)

Expand All @@ -95,77 +96,10 @@ build_tree_from_concepts <- function(concepts, counts) {
stateLeafs <- list(opened = TRUE, selected = TRUE)
nLeafs <- tree$leafCount
tree$Set(state = rep(list(stateLeafs), nLeafs), filterFun = isLeaf)
# seems impossible to have tree opened and selected from tree.data object
#stateNotLeafs <- list(opened = TRUE)
#tree$Set(state = rep(list(stateNotLeafs),length(tree)-nLeafs), filterFun = isNotLeaf)
# "state": {
# "opened": true,
# "disabled": false,
# "selected": false,
# "loaded": false
# }
#tree$Do(function(node) node$state = list(opened = TRUE, disabled = FALSE, selected = TRUE, loaded = FALSE))

#tree = lapply(tree, function(x) structure(x, stopened = T))

return(tree)
}


# -----------------------------------------------------------------------------
# OBSERVATIONS
# -----------------------------------------------------------------------------

## EVENTUALLY CONVERT PLOT INTO A FUNCTION


# -----------------------------------------------------------------------------
# INTERSECTION
# -----------------------------------------------------------------------------

# # check which observations are in which layers
# intersect_observations_to_layers <- function(layer, obs) {
# # per feature
# for (i in 1:nrow(layer)){
# # json
# # name is in properties
# #j <- unlist(f[[i]])
# f01 <- layer[i,]
#
# label <- f01$NAME
#
# # make sure coordinate systems are the same
# # we actually overwrite the features crs so this could be wrong...
# f01 <- st_set_crs(f01, st_crs(obs))
# # drop z dimension
# f01 <- st_zm(f01)
# # seems most MULTIPOLYGONS are POLYGONS at the lower level
# f01 <- st_make_valid(f01)
#
# # f01$geometry <- f01$geometry %>%
# # s2::s2_rebuild() %>%
# # sf::st_as_sfc()
#
# # check which points intersect with polygon
# tryCatch({
# # do not use s2
# sf::sf_use_s2(FALSE)
# lst <- st_intersects(obs, f01, sparse = FALSE)
# message(paste("LAYER ", label, " is OK"))
# sf::sf_use_s2(TRUE)
# # fill in the name for these points
# if (sum(lst) > 0) {
# obs[lst,]$area <- label
# }
# },
# #error
# error = function(cond) message(paste("LAYER ", label, " has issues"))
# ) #tryCatch
# }
# return(obs)
# }


# -----------------------------------------------------------------------------
# VISUALIZATIONS
# -----------------------------------------------------------------------------
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