Make an Illumina microarray control-probe QC plot with plot_ly()

Averages a fixed set of Illumina control probe groups (cy3 dilution series, stringency, negative, biotin, labeling and housekeeping controls) across samples and plots them as lines, following the standard QC relationships between groups (see illuminaarrayqcInput's displayed checklist: cy3_high > cy3_med > cy3_low, low stringency =~ 0, high stringency <= cy3 high, housekeeping/biotin = high, negative =~ 0).

Usage

interactive_illumina_control_probes(
  control_annotation,
  controls,
  sample_order = NULL
)

Arguments

control_annotation

Data frame of control probe annotation, with an Array_Address_Id column matching the row names of controls and a Reporter_Group_id column identifying each control probe group

controls

Matrix of control probe intensities, control probes (by Array_Address_Id) by row, samples by column

sample_order

Character vector giving the sample (x axis) display order. Defaults to colnames(controls)

Value

output A plotly htmlwidget

Examples

control_annotation <- data.frame(
  Array_Address_Id = paste0("probe", 1:9),
  Reporter_Group_id = c(
    "phage_lambda_genome:low", "phage_lambda_genome:med", "phage_lambda_genome:high",
    "phage_lambda_genome:pm", "phage_lambda_genome:mm2", "permuted_negative",
    "phage_lambda_genome", "thrB", "housekeeping"
  )
)
controls <- matrix(runif(9 * 3, 1, 1000),
  nrow = 9, dimnames = list(control_annotation$Array_Address_Id, paste0("sample", 1:3))
)

interactive_illumina_control_probes(control_annotation, controls)