In jmbuhr/ShinyLipids: ShinyLipids

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

So what happens to my data?...

you might rightfully ask yourself when loading a dataset into ShinyLipids. Luckily, we expose the internals of ShinyLipids in the form of clearly named functions for you to use even outside of the app. If you want to learn more about how exactly things work underneath the hood, you can click at the individual functions to read their documentation or have a look at the source code. But for now, let's explore the example data together. We will follow the steps that ShinyLipids takes and inspect intermediate results.

First, we load ShinyLipids

library(ShinyLipids)

input <- defaultInput()

We can get the file path to our example data, given that ShinyLipids is installed, and open up a database connection to the database dump file

path <- system.file("extdata/exampleDatabase.db", package = "ShinyLipids")
databaseConnection <- DBI::dbConnect(RSQLite::SQLite(), path)

We see, that our example file contains two tables (their names are mandatory).

DBI::dbListTables(databaseConnection)

From this connection, we load in our meta data "id_info" -- information about the dataset(s) in the "data2" table:

metaData <- collectMetaData(databaseConnection)
metaData

We see, that our ownly dataset in the database has id 1, so we use that id to collect the raw data and inspect the first 6 rows:

rawData <- collectRawData(con = databaseConnection,
                          id = 1)
head(rawData)

Next, we run the data processing steps.

plotData <- rawData %>%
  imputeMissingIf(input) %>% 
  addLipidProperties() %>% 
  standardizeWithinTechnicalReplicatesIf(input) %>%
  filterRawDataFor(input) %>%
  standardizeWithin(input) %>%
  createPlotData(input)

head(plotData)

meanPlotData <- summarisePlotData(plotData, input)
head(meanPlotData)

plt <- createMainPlot(plotData            = plotData,
                      meanPlotData        = meanPlotData,
                      pairwiseComparisons = NULL,
                      input = input)

plt

jmbuhr/ShinyLipids documentation built on June 25, 2021, 2:26 a.m.