## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)

## ----sampleDataFrame----------------------------------------------------------
df <- data.frame(protein_Id = c("tr|A|HUMAN","tr|B|HUMAN","tr|C|HUMAN","tr|D|HUMAN"),
                 Intensity_A = c(100,10000,10,NA),
                 Intensity_B = c(NA, 9000, 20, 100),
                 Intensity_C = c(200,8000,NA,150),
                 Intensity_D = c(130,11000, 50, 50))
df



## ----pivot2Long---------------------------------------------------------------
table_long <- tidyr::pivot_longer(df, starts_with("Intensity_"),names_to = "Sample", values_to = "Intensity")
table_long

## ----annotationDataFrame------------------------------------------------------
annot <- data.frame(Sample = c("Intensity_A", "Intensity_B", "Intensity_C", "Intensity_D"), Group = c("A","A","B","C"))

## ----addAnnotation------------------------------------------------------------
table_long <- dplyr::inner_join(annot, table_long)

## ----createConfig-------------------------------------------------------------
config <- prolfqua::AnalysisConfiguration$new()
config$file_name = "Sample"
config$work_intensity = "Intensity"


## ----addFactors---------------------------------------------------------------
config$hierarchy[["protein_Id"]]    <-  "protein_Id"
config$factors[["Group"]] <- "Group"


## ----buildLFQData-------------------------------------------------------------
analysis_data <- prolfqua::setup_analysis(table_long, config)
lfqdata <- prolfqua::LFQData$new(analysis_data, config)

## ----basicPlotting------------------------------------------------------------
lfqdata$hierarchy_counts()
smrz <- lfqdata$get_Summariser()
smrz$plot_hierarchy_counts_sample()

## ----readInData---------------------------------------------------------------
dataLongFormat <- prolfqua::sim_lfq_data(Nprot = 20, PEPTIDE = TRUE)
head(dataLongFormat)

## ----defineAnalysisTable------------------------------------------------------
config <- prolfqua::AnalysisConfiguration$new()
config$file_name = "sample"
config$work_intensity = "abundance"


## ----defineHierarchyAndFactors------------------------------------------------
config$hierarchy[["proteinID"]]    <-  "proteinID"
config$hierarchy[["peptideID"]]    <-  "peptideID"
config$factors[["group"]] <- "group"

## ----mateDataAndConfig--------------------------------------------------------
analysis_data <- prolfqua::setup_analysis(dataLongFormat, config)

lfq_tmp <- prolfqua::LFQData$new(analysis_data, config)
lfq_tmp$summarize_hierarchy()


## ----generateLFQData----------------------------------------------------------
lfqdata <- prolfqua::LFQData$new(analysis_data, config)

## ----doBarPlotPerSample, fig.cap="Shown are how many precursors or proteins are found in each sample", fig.align=5, fig.height=5----
smrz <- lfqdata$get_Summariser()
smrz$plot_hierarchy_counts_sample()

## ----session_info-------------------------------------------------------------
sessionInfo()