Nothing
## ----include = FALSE----------------------------------------------------------
test_protti <- identical(Sys.getenv("TEST_PROTTI"), "true")
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, eval = test_protti, message = FALSE, warning = FALSE--------------
# library(protti)
# library(magrittr)
# library(dplyr)
## ----create_synthetic_data, eval = test_protti--------------------------------
# # by setting the seed we are making sure that the random object generation can be reproduced
# set.seed(123)
#
# data <- create_synthetic_data(
# n_proteins = 100,
# frac_change = 0.05,
# n_replicates = 3,
# n_conditions = 2,
# method = "effect_random",
# additional_metadata = TRUE
# )
## ----qc_cvs, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# input <- data %>%
# # as the data is log2 transformed, we need to transform it back before calculating the CVs
# mutate(raw_intensity = 2^peptide_intensity_missing)
#
# qc_cvs(
# data = input,
# grouping = peptide,
# condition = condition,
# intensity = raw_intensity,
# plot = FALSE
# )
#
# qc_cvs(
# data = input,
# grouping = peptide,
# condition = condition,
# intensity = raw_intensity,
# plot = TRUE,
# plot_style = "violin"
# )
## ----qc_ids, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_ids(
# data = input,
# sample = sample,
# grouping = protein,
# intensity = peptide_intensity_missing,
# condition = condition,
# plot = FALSE
# )
#
# qc_ids(
# data = input,
# sample = sample,
# grouping = protein,
# intensity = peptide_intensity_missing,
# condition = condition,
# title = "Protein identifications per sample",
# plot = TRUE
# )
## ----qc_peptide_type, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_peptide_type(
# data = input,
# sample = sample,
# peptide = peptide,
# pep_type = pep_type,
# method = "intensity",
# intensity = raw_intensity,
# plot = TRUE,
# interactive = FALSE
# )
#
# qc_peptide_type(
# data = input,
# sample = sample,
# peptide = peptide,
# pep_type = pep_type,
# method = "count",
# plot = TRUE,
# interactive = FALSE
# )
## ----qc_intensity_distribution_boxplot, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_intensity_distribution(
# data = input,
# sample = sample,
# grouping = peptide,
# intensity_log2 = peptide_intensity_missing,
# plot_style = "boxplot"
# )
#
# qc_median_intensities(
# data = input,
# sample = sample,
# grouping = peptide,
# intensity = peptide_intensity_missing
# )
## ----qc_charge_states, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_charge_states(
# data = input,
# sample = sample,
# grouping = peptide,
# charge_states = charge,
# method = "intensity",
# intensity = raw_intensity,
# plot = TRUE
# )
## ----qc_missed_cleavages, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_missed_cleavages(
# data = input,
# sample = sample,
# grouping = peptide,
# missed_cleavages = n_missed_cleavage,
# method = "intensity",
# intensity = raw_intensity,
# plot = TRUE
# )
## ----qc_sequence_coverage, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_sequence_coverage(
# data = input,
# protein_identifier = protein,
# coverage = coverage
# )
## ----qc_peak_width, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_peak_width(
# data = input,
# sample = sample,
# intensity = peptide_intensity_missing,
# retention_time = retention_time,
# peak_width = peak_width
# )
## ----qc_data_completeness, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_data_completeness(
# data = input,
# sample = sample,
# grouping = peptide,
# intensity = peptide_intensity_missing,
# plot = TRUE
# )
## ----qc_intensity_distribution_histogram, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_intensity_distribution(
# data = input,
# grouping = peptide,
# intensity_log2 = peptide_intensity_missing,
# plot_style = "histogram"
# )
## ----qc_sample_correlation, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_sample_correlation(
# data = input,
# sample = sample,
# grouping = peptide,
# intensity_log2 = peptide_intensity_missing,
# condition = condition,
# interactive = FALSE
# )
## ----qc_pca, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# qc_pca(
# data = data,
# sample = sample,
# grouping = peptide,
# intensity = peptide_intensity_missing,
# condition = condition,
# digestion = NULL,
# plot_style = "scree"
# )
#
# qc_pca(
# data = data,
# sample = sample,
# grouping = peptide,
# intensity = peptide_intensity_missing,
# condition = condition,
# components = c("PC1", "PC2"),
# plot_style = "pca"
# )
## ----qc_ranked_intensities, eval = test_protti, fig.width = 6, fig.height = 4, fig.align = "center"----
# # Plot ranked peptide intensities
# qc_ranked_intensities(
# data = data,
# sample = sample,
# grouping = peptide,
# intensity_log2 = peptide_intensity,
# plot = TRUE,
# )
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