olink_bridgeability_plot: Plots for each bridgeable assays between two platforms /...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Plots for each bridgeable assays between two platforms / products Author : Amrita Kar

Description

Generates a combined plot per assay containing a violin and boxplot plot for IQR ranges ; correlation plot of NPX values ; a median count bar plot and KS plots from 2 platforms

Usage

olink_bridgeability_plot(data, median_counts_threshold = 150, min_count = 10)

Arguments

data	data frame of cross-product bridge normalized data generated by olink_normalization()
median_counts_threshold	Numeric value to use for median counts threshold for the two platforms. Default is 150
min_count	Numeric value to use for minimum counts for the two platforms. Default is 10

Value

An object of class "ggplot", 4 combined plots for each protein.

Examples

npx_ht <- OlinkAnalyze:::data_ht_small |>
 dplyr::filter(SampleType == "SAMPLE") |>
 dplyr::mutate(Project = "data1")

npx_3072 <- OlinkAnalyze:::data_3k_small |>
 dplyr::filter(SampleType == "SAMPLE") |>
 dplyr::mutate(Project = "data2")

overlapping_samples <- unique(intersect(npx_ht |>
                                         dplyr::distinct(SampleID) |>
                                         dplyr::pull(),
                                       npx_3072 |>
                                         dplyr::distinct(SampleID) |>
                                         dplyr::pull()))

data <- OlinkAnalyze::olink_normalization(df1 = npx_ht,
                                         df2 = npx_3072,
                                         overlapping_samples_df1 =
                                           overlapping_samples,
                                         df1_project_nr = "Explore HT",
                                         df2_project_nr = "Explore 3072",
                                         reference_project = "Explore HT")

olinkids <- unique(paste0(data$OlinkID,"_",data$Assay))
results <- olink_bridgeability_plot(data = data,
                          median_counts_threshold = 150,
                          min_count = 10)
names(results) <- olinkids

OlinkAnalyze documentation built on April 4, 2025, 3:26 a.m.