Commit aace7b66 authored by dmattek's avatar dmattek

Added: setNumericRounding(2)

parent d5ab749a
......@@ -23,16 +23,23 @@ library(ggthemes) # nice colour palettes
library(sparcl) # sparse hierarchical and k-means
library(dtw) # for dynamic time warping
library(factoextra) # extract and visualize the output of multivariate data analyses
library(imputeTS) # for interpolating NAs
library(robust) # for robust linear regression
library(MASS)
library(pracma) # for trapz
library(pracma) # for trapz used in AUC calculation
# Global parameters ----
# change to increase the limit of the upload file size
options(shiny.maxRequestSize = 200 * 1024 ^ 2)
# Important when joining, grouping or ordering numeric (i.e. double, POSIXct) columns.
# https://stackoverflow.com/questions/58230619/xy-join-of-keyed-data-table-fails-when-key-on-numeric-column-and-data-fread-fr
setNumericRounding(2)
# colour of loader spinner (shinycssloaders)
options(spinner.color="#00A8AA")
......@@ -67,7 +74,7 @@ shinyServer(function(input, output, session) {
if (DEB)
cat("server:dataGen1\n")
return(LOCgenTraj(in.nwells = 3, in.addout = 3))
return(LOCgenTraj2())
})
# Load main data file
......@@ -349,7 +356,7 @@ shinyServer(function(input, output, session) {
choices = list('fold-change' = 'mean', 'z-score' = 'z.score'),
width = "40%"
),
bsTooltip('rBnormMeth', helpText.server[12], placement = "top", trigger = "hover", options = NULL)
bsTooltip('rBnormMeth', helpText.server[["rBnormMeth"]], placement = "top", trigger = "hover", options = NULL)
)
}
})
......@@ -377,7 +384,7 @@ shinyServer(function(input, output, session) {
value = c(locRTmin, 0.1 * locRTmax),
step = 1
),
bsTooltip('slNormRtMinMax', helpText.server[13], placement = "top", trigger = "hover", options = NULL)
bsTooltip('slNormRtMinMax', helpText.server[["slNormRtMinMax"]], placement = "top", trigger = "hover", options = NULL)
)
}
})
......@@ -393,7 +400,7 @@ shinyServer(function(input, output, session) {
label = 'Robust stats',
FALSE,
width = "40%"),
bsTooltip('chBnormRobust', helpText.server[14], placement = "top", trigger = "hover", options = NULL)
bsTooltip('chBnormRobust', helpText.server[["chBnormRobust"]], placement = "top", trigger = "hover", options = NULL)
)
}
})
......@@ -409,7 +416,7 @@ shinyServer(function(input, output, session) {
label = 'Normalisation grouping',
choices = list('Entire dataset' = 'none', 'Per group' = 'group', 'Per trajectory' = 'id'),
width = "40%"),
bsTooltip('chBnormGroup', helpText.server[15], placement = "top", trigger = "hover", options = NULL)
bsTooltip('chBnormGroup', helpText.server[["chBnormGroup"]], placement = "top", trigger = "hover", options = NULL)
)
}
})
......@@ -420,7 +427,7 @@ shinyServer(function(input, output, session) {
"alDataFormat",
title = "Data format",
content = helpText.server[["alDataFormat"]],
trigger = "click", )
trigger = "click")
# Processing-data ----
......@@ -761,8 +768,12 @@ shinyServer(function(input, output, session) {
setkeyv(loc.out, c(COLGR, COLID, COLRT))
if (input$chBtrajInter) {
# here we fill missing data with NA's
loc.out = loc.out[setkeyv(loc.out[, .(seq(min(get(COLRT), na.rm = T), max(get(COLRT), na.rm = T), input$inSelTimeFreq)), by = c(COLGR, COLID)], c(COLGR, COLID, 'V1'))]
# here we fill missing rows with NA's
loc.out = loc.out[setkeyv(loc.out[,
.(seq(min(get(COLRT), na.rm = T),
max(get(COLRT), na.rm = T),
input$inSelTimeFreq)),
by = c(COLGR, COLID)], c(COLGR, COLID, 'V1'))]
# x-check: print all rows with NA's
if (DEB) {
......@@ -959,6 +970,9 @@ shinyServer(function(input, output, session) {
###### Scatter plot
callModule(tabScatterPlot, 'tabScatter', data4trajPlotNoOut, in.fname = function() return(FPDFSCATTER))
##### Hierarchical estimation
callModule(clustValid, 'tabClValid', data4clust)
##### Hierarchical clustering
callModule(clustHier, 'tabClHier', data4clust, data4trajPlotNoOut, data4stimPlot)
......
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