Reference

Data processing

Functions that read in data from the database and process it. This includes filtering, standardization and calculation of summaries.

collectMetaData()

Collect metadata from database

collectLipidClassOrder()

Lipid Class Order

collectRawData()

Collect raw data from database

addLipidProperties()

Add Lipid properties

imputeMissingIf()

Impute implicit missing values as 0

standardizeWithinTechnicalReplicatesIf()

Standardize data within technical replicates

filterRawDataFor()

Filter raw data

standardizeWithin()

Standardize raw data

createPlotData()

Create the data ready for plotting

summarisePlotData()

Summarise the plot data

doAllPairwiseComparisons()

Test all possible pairwise t-tests

createPcaPrep()

Create prepped pca recipe

createWideData()

Create wide data

Main user facing functions

The main entry points for (new) users

run_app()

Run the Shiny Application

createDatabase()

Create your own database

Plotting functions

Functions to generate plots

createMainPlot()

Create the main plot

createHeatmap()

Create a Heatmap from data

mainTheme()

mainTheme

Utility functions

Smaller helper utilities

defaultInput()

Generate list of default options

createQueryForID()

Generate SQL Query for the selected dataset

updateAllRangeInputs()

Custom update range input

updateAllSelectizeInputs()

Custom update selectize input

mainScale()

Create color scale

parseDate()

Make a date

testAllMoreThanOneReplicate()

Test that all samples have more than one replicate

filterIfNotNull()

Filter if not null

testPairwise()

Pairwise t-tests