Plot Eplet Results from SPI Assay

This function reads in SAB (single antigen bead) results (either as a data frame or as a file path to a CSV/XLS/XLSX file), processes the data to quantify eplet-specific positivity based on a specified MFI cutoff, and then generates one of three plot types: a treemap, a bar plot, or an AUC plot. The eplet annotations are joined from an internal database, and the resulting plot is colored by evidence level.

Usage

plotEplets(
  result_file,
  cutoff = 2000,
  evidence_level = c("A1", "A2"),
  group_by = "eplet",
  eplet_filter = 3,
  percPos_filter = 0.4,
  plot_type = c("treemap", "bar", "AUC"),
  cut_min = 250,
  cut_max = 10000,
  cut_step = 250,
  top_eplets = 10,
  palette = "spectral",
  ...
)

Arguments

result_file

A data frame containing SAB results or a character string specifying the path to a SAB file in CSV, XLS, or XLSX format.

cutoff

Numeric. Threshold for MFI to separate positive and negative beads. Default is 2000.

evidence_level

Character vector indicating the antibody reactivity levels to keep. Defaults to c("A1", "A2"), which represent antibody-confirmed eplets. Other acceptable levels include "B", "D", or NULL to apply no filter.

group_by

A character string or indicating the coloring grouping for the plot, default is `eplet`. Other options include `loci` or `evidence_level`.

eplet_filter

Integer. (Only used when plot_type = "AUC") Specifying the minimum number of times an eplet must appear in the assay before calculating the AUC. Defaults to `3`.

percPos_filter

Numeric value. (Only used when plot_type = "AUC") Value between 0 and 1 specifying the minimum relative proportion of positive beads (per eplet) to include in the final summary. Eplets with a proportion below this threshold are excluded. Defaults to 0.4.

plot_type

Character. Type of plot to generate. Must be one of "treemap", "bar", or "AUC". Defaults to "treemap".

cut_min

Integer. (Only used when plot_type = "AUC") The minimum MFI cutoff value. Defaults to 250.

cut_max

Integer. (Only used when plot_type = "AUC") The maximum MFI cutoff value. Defaults to 10000.

cut_step

Integer. (Only used when plot_type = "AUC") The increment step between the minimum and maximum MFI cutoff values. Defaults to 250.

top_eplets

Integer. The maximum number of top eplets to display in the bar or AUC plot. Defaults to 10.

palette

Character. A color palette name (from hcl.pals) or a custom palette function to use for the plot. Defaults to "spectral".

...

Additional arguments passed to the ggplot theme

Value

A ggplot object visualizing eplet counts (or AUC values) according to the specified parameters.

Examples

# Using a data frame:
plotEplets(deepMatchR_example[[1]], 
           cutoff = 2000, 
           evidence_level = c("A1", "A2", "B"),
           percPos_filter = 0.4, 
           plot_type = "treemap")