OlinkAnalyze (version 4.3.0)

olink_bridgeability_plot: Plots for each bridgeable assays between two products.

Description

Plots for each bridgeable assays between two products.

Usage

olink_bridgeability_plot(
  data,
  olink_id = NULL,
  median_counts_threshold = 150L,
  min_count = 10L
)

Value

An object of class "ggplot" containing 4 plots for each assay.

Arguments

data

A tibble containing the cross-product bridge normalized dataset generated by olink_normalization.

olink_id

Character vector of Olink assay identifiers OlinkID for which bridgeability plots will be created. If null, plots for all assays in data will be created. (default = NULL)

median_counts_threshold

Threshold indicating the minimum median counts for each product (default = 150).

min_count

Threshold indicating the minimum number of counts per data point (default = 10). Data below min_count are excluded.

Author

Amrita Kar Klev Diamanti

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

Examples

# \donttest{
npx_ht <- OlinkAnalyze:::data_ht_small |>
  dplyr::filter(
    .data[["SampleType"]] == "SAMPLE"
  )

npx_3072 <- OlinkAnalyze:::data_3k_small |>
  dplyr::filter(
    .data[["SampleType"]] == "SAMPLE"
  )

overlapping_samples <- intersect(
  x = npx_ht$SampleID,
  y = npx_3072$SampleID
)

data_norm <- 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"
)

data_norm_bridge_p <- OlinkAnalyze::olink_bridgeability_plot(
  data = data_norm,
  olink_id = c("OID40770", "OID40835"),
  median_counts_threshold = 150L,
  min_count = 10L
)
# }