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shiny-timecourse-inspector
Commit f544f945 authored by dmattek's avatar dmattek
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Changed checks for NULL data to validate-need syntax.Uses custom nbclust functions. DTW is back.

parent d216d802
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Showing with 113 additions and 105 deletions
modules/tabClValid.R
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......@@ -5,7 +5,8 @@
# This module is a tab for hierarchical clustering (base R hclust + dist)
helpText.clValid = c(alertClValidNAsPresent = paste0("NAs present. The selected distance measure will work, ",
"however caution is recommended. Consider interpolation of NAs and missing data in the left panel."),
"however PCA will not be avaliable."),
alertClValidNAsPresentDTW = paste0("NAs present. DTW distance measure will NOT work."),
alLearnMore = paste0("<p><a href=http://www.sthda.com/english/wiki/print.php?id=241 title=\"External link\">Clustering</a> ",
"is an <b>unsupervised</b> machine learning method for partitioning ",
"dataset into a set of groups or clusters. The procedure will return clusters ",
......@@ -60,7 +61,8 @@ clustValidUI <- function(id, label = "Validation") {
choices = list("Euclidean" = "euclidean",
"Manhattan" = "manhattan",
"Maximum" = "maximum",
"Canberra" = "canberra"),
"Canberra" = "canberra",
"DTW" = "DTW"),
selected = "euclidean"
),
bsAlert("alertAnchorClValidNAsPresent")
......@@ -134,27 +136,39 @@ clustValidUI <- function(id, label = "Validation") {
)
),
br(),
withSpinner(plotOutput(ns('outPlotClPCA'))),
br(),
withSpinner(plotOutput(ns('outPlotTree'))),
br(),
withSpinner(plotOutput(ns('outPlotSilhForCut')))
withSpinner(plotOutput(ns('outPlotSilhForCut'))),
br(),
withSpinner(plotOutput(ns('outPlotClPCA')))
)
)
)
}
# SERVER ----
clustValid <- function(input, output, session, in.data4clust) {
clustValid <- function(input, output, session, in.dataWide) {
ns = session$ns
# Return the number of clusters from the slider
# and delay by a constant in milliseconds defined in auxfunc.R
returnNclust = reactive({
return(input$slClValidNclust)
}) %>% debounce(MILLIS)
# Return max number of clusters from the slider
# and delay by a constant in milliseconds defined in auxfunc.R
returnMaxNclust = reactive({
return(input$slClValidMaxClust)
}) %>% debounce(MILLIS)
# calculate distance matrix for further clustering
# time series arranged in rows with columns corresponding to time points
userFitDistHier <- reactive({
cat(file = stderr(), 'clustValid:userFitDistHier \n')
calcDist <- reactive({
cat(file = stderr(), 'clustValid:calcDist \n')
loc.dm = in.data4clust()
loc.dm = in.dataWide()
if (is.null(loc.dm)) {
return(NULL)
......@@ -163,70 +177,52 @@ clustValid <- function(input, output, session, in.data4clust) {
# Throw some warnings if NAs present in the dataset.
# DTW cannot compute distance when NA's are preset.
# Other distance measures can be calculated but caution is required with interpretation.
print(sum(is.na(loc.dm)))
# NAs in the wide format can result from explicit NAs in the measurment column or
# from missing rows that cause NAs to appear when convertinf from long to wide (dcast)
if(sum(is.na(loc.dm)) > 0) {
if (input$selectDiss == "DTW") {
createAlert(session, "alertAnchorClValidNAsPresent", "alertClValidNAsPresentDTW", title = "Error",
content = helpText.clValid[["alertClValidNAsPresentDTW"]],
append = FALSE,
style = "danger")
closeAlert(session, 'alertClValidNAsPresent')
return(NULL)
} else {
createAlert(session, "alertAnchorClValidNAsPresent", "alertClValidNAsPresent", title = "Warning",
content = helpText.clValid[["alertClValidNAsPresent"]],
append = FALSE,
style = "warning")
closeAlert(session, 'alertClValidNAsPresentDTW')
}
} else {
closeAlert(session, 'alertClValidNAsPresentDTW')
closeAlert(session, 'alertClValidNAsPresent')
}
}
# calculate distance matrix
return(dist(loc.dm, method = input$selectPlotHierDiss))
# calculate distance matrix
return(proxy::dist(loc.dm, method = input$selectDiss))
})
# calculate dendrogram for a chosen number of clusters and the linkage method
calcDendCut = reactive({
cat(file = stderr(), 'clustValid:calcDendCut \n')
loc.dm = returnDMwithChecks()
loc.dist = calcDist()
if (is.null(loc.dm)) {
if (is.null(loc.dist)) {
return(NULL)
}
return(factoextra::eclust(x = loc.dm,
return(factoextra::hcut(x = loc.dist,
k = returnNclust(),
FUNcluster = "hclust",
k = input$slClValidNclust,
hc_method = input$selectLinkage,
hc_metric = input$selectDiss,
graph = FALSE))
})
# Return a matrix with time series in wide format
# If data contains NAs (from explicit NAs or due to missing time points,
# or due to missing time points after outlier removal),
# some warnings are thrown. E.g. DTW cannot caluclate distance if NAs are present.
returnDMwithChecks = reactive({
cat(file = stderr(), 'clustValid:returnDMwithChecks \n')
loc.dm = in.data4clust()
if (is.null(loc.dm)) {
return(NULL)
}
# Throw some warnings if NAs present in the dataset.
# DTW cannot compute distance when NA's are preset.
# Other distance measures can be calculated but caution is required with interpretation.
print(sum(is.na(loc.dm)))
if(sum(is.na(loc.dm)) > 0) {
createAlert(session, "alertAnchorClValidNAsPresent", "alertClValidNAsPresent",
title = "Warning",
content = helpText.clValid[["alertClValidNAsPresent"]],
append = FALSE,
style = "warning")
} else {
closeAlert(session, 'alertClValidNAsPresent')
}
return(loc.dm)
})
# Plotting ----
# Function instead of reactive as per:
# http://stackoverflow.com/questions/26764481/downloading-png-from-shiny-r
......@@ -234,23 +230,22 @@ clustValid <- function(input, output, session, in.data4clust) {
# plot average silhouette
plotSilhAvg <- function() {
locBut = input$butPlotRel
if (locBut == 0) {
cat(file = stderr(), 'plotSilhAvg: Go button not pressed\n')
return(NULL)
}
cat(file = stderr(), 'plotSilhAvg: in\n')
loc.dm = returnDMwithChecks()
if (is.null(loc.dm)) {
return(NULL)
}
loc.p = factoextra::fviz_nbclust(loc.dm,
hcut,
# make the f-n dependent on the button click
locBut = input$butPlotRel
# Check if required data exists
# Thanks to isolate all mods in the left panel are delayed
# until clicking the Plot button
loc.dist = isolate(calcDist())
validate(
need(!is.null(loc.dist), "Nothing to plot. Load data first!")
)
loc.p = LOCnbclust(loc.dist,
method = "silhouette",
k.max = input$slClValidMaxClust,
k.max = returnMaxNclust(),
hc_metric = input$selectDiss,
hc_method = input$selectLinkage) +
xlab("Number of clusters") +
......@@ -266,23 +261,22 @@ clustValid <- function(input, output, session, in.data4clust) {
# plot Ws
plotWss <- function() {
cat(file = stderr(), 'plotWss: in\n')
# make the f-n dependent on the button click
locBut = input$butPlotRel
if (locBut == 0) {
cat(file = stderr(), 'plotWss: Go button not pressed\n')
return(NULL)
}
loc.dm = returnDMwithChecks()
if (is.null(loc.dm)) {
return(NULL)
}
# Check if required data exists
# Thanks to isolate all mods in the left panel are delayed
# until clicking the Plot button
loc.dist = isolate(calcDist())
validate(
need(!is.null(loc.dist), "Nothing to plot. Load data first!")
)
loc.p = factoextra::fviz_nbclust(loc.dm,
hcut,
loc.p = LOCnbclust(loc.dist,
method = "wss",
k.max = input$slClValidMaxClust,
k.max = returnMaxNclust(),
hc_metric = input$selectDiss,
hc_method = input$selectLinkage) +
xlab("Number of clusters") +
......@@ -299,18 +293,18 @@ clustValid <- function(input, output, session, in.data4clust) {
# plot dendrogram tree
plotTree <- function() {
cat(file = stderr(), 'plotTree: in\n')
# make the f-n dependent on the button click
locBut = input$butPlotInt
if (locBut == 0) {
cat(file = stderr(), 'plotTree: Go button not pressed\n')
return(NULL)
}
loc.part = calcDendCut()
if (is.null(loc.part)) {
return(NULL)
}
# Check if required data exists
# Thanks to isolate all mods in the left panel are delayed
# until clicking the Plot button
loc.part = isolate(calcDendCut())
validate(
need(!is.null(loc.part), "Nothing to plot. Load data first!")
)
loc.p = factoextra::fviz_dend(loc.part,
show_labels = F,
......@@ -329,42 +323,56 @@ clustValid <- function(input, output, session, in.data4clust) {
# PCA visualization of partitioning methods
plotClPCA <- function() {
cat(file = stderr(), 'plotTree: in\n')
# make the f-n dependent on the button click
locBut = input$butPlotInt
if (locBut == 0) {
cat(file = stderr(), 'plotClPCA: Go button not pressed\n')
return(NULL)
}
loc.part = calcDendCut()
if (is.null(loc.part)) {
# Check if required data exists
# Thanks to isolate all mods in the left panel are delayed
# until clicking the Plot button
loc.part = isolate(calcDendCut())
loc.dm = in.dataWide()
print(sum(is.na(loc.dm)))
validate(
need(!is.null(loc.part), "Nothing to plot. Load data first!"),
need(!is.null(loc.dm), "Nothing to plot. Load data first!"),
need(sum(is.na(loc.dm)), "Cannot calculate PCA in the presence of missing data and/or NAs.")
)
if (sum(is.na(loc.dm)) > 0)
return(NULL)
}
loc.p = factoextra::fviz_cluster(loc.part,
data = loc.dm,
geom = "point",
elipse.type = "norm",
elipse.type = "convex",
main = "Principle components"
)
)+
LOCggplotTheme(in.font.base = PLOTFONTBASE,
in.font.axis.text = PLOTFONTAXISTEXT,
in.font.axis.title = PLOTFONTAXISTITLE,
in.font.strip = PLOTFONTFACETSTRIP,
in.font.legend = PLOTFONTLEGEND)
return(loc.p)
}
# plot silhouetts for a particular dendrogram cut
plotSilhForCut <- function() {
cat(file = stderr(), 'plotSilhForCut: in\n')
# make the f-n dependent on the button click
locBut = input$butPlotInt
if (locBut == 0) {
cat(file = stderr(), 'plotSilhForCut: Go button not pressed\n')
return(NULL)
}
loc.part = calcDendCut()
if (is.null(loc.part)) {
return(NULL)
}
# Check if required data exists
# Thanks to isolate all mods in the left panel are delayed
# until clicking the Plot button
loc.part = isolate(calcDendCut())
validate(
need(!is.null(loc.part), "Nothing to plot. Load data first!")
)
loc.p = factoextra::fviz_silhouette(loc.part,
print.summary = FALSE,
......
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