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Title:

Read .Q-View Multiplex ELISA Project Files

Version:

1.0.0

Description:

Pure-R parser for the binary '.Q-View' project file format used in chemiluminescent multiplex ELISA plate imaging and quantification. Reads the embedded H2 database container and CSV report, and returns project metadata, the analyte panel with units and detection limits, sample well-group assignments, per-well pixel-intensity replicates, summary statistics, optional back-calculated concentrations, and a plate layout, all as tidy tibbles. No Java runtime or H2 database driver is required.

License:

MIT + file LICENSE

URL:

https://github.com/CTTIR/qviewparsR, https://cttir.github.io/qviewparsR/

BugReports:

https://github.com/CTTIR/qviewparsR/issues

Depends:

R (≥ 4.1.0)

Imports:

cli, dplyr, lifecycle, openxlsx2, readr, rlang, stats, tibble, tidyr, tools, utils

Suggests:

bslib, chromote, DT, ggplot2, knitr, patchwork, rmarkdown, shiny, shinytest2, testthat (≥ 3.0.0), withr

VignetteBuilder:

knitr

Config/testthat/edition:

Encoding:

UTF-8

Language:

en-US

Config/roxygen2/version:

8.0.0

Config/Needs/website:

CTTIR/themakR

NeedsCompilation:

Packaged:

2026-07-16 11:49:44 UTC; rh

Author:

R. Heller

[aut, cre, cph], M. Mannes

[aut, cph]

Maintainer:

R. Heller <raban.heller@uni-ulm.de>

Repository:

CRAN

Date/Publication:

2026-07-23 13:50:08 UTC

qviewparsR: Read .Q-View Multiplex ELISA Project Files

Description

Pure-R parser for .Q-View binary project files used in chemiluminescent multiplex ELISA plate imaging and quantification. Extracts pixel intensities, analyte mappings, sample assignments, plate layout, optional curve-fit parameters, and the embedded CSV report from the H2 database container format. Returns tidy tibbles ready for downstream statistical analysis.

Main functions

Reader: read_qview() – parse a .Q-View file.
Helpers: strip_qview_prefix() reverse the Q-View internal naming convention; well_label() map (row, column) to plate notation.
Optional: read_qview_template() parse a Q-View well-assignment template CSV.
Methods: is_qview(), print.qview(), plot.qview(), as_tibble.qview().
Shiny: qview_app() interactive upload / preview / download.

Author(s)

Maintainer: R. Heller raban.heller@uni-ulm.de (ORCID) [copyright holder]

Authors:

R. Heller raban.heller@uni-ulm.de (ORCID) [copyright holder]
M. Mannes (ORCID) [copyright holder]

Coerce a Q-View object to a tibble

Description

Returns the long-format pixel_intensities table — the primary tabular data carried by a qview object. To access other slots (well groups, analyte panel, summary statistics) use ⁠qv$<slot>⁠ directly.

Usage

## S3 method for class 'qview'
as_tibble(x, ...)

Arguments

x

A qview object returned by read_qview().

...

Unused; for S3 generic compatibility.

Value

A tibble::tibble() of replicate pixel-intensity readings.

Examples

path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path, verbose = FALSE)
tibble::as_tibble(qv)

Test whether an object is a `qview`

Description

Usage

is_qview(x)

Arguments

x

An object to test.

Value

Logical scalar.

Examples

path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
is_qview(read_qview(path, verbose = FALSE))
is_qview(list())

Plot a Q-View object

Description

Quick-look plots for a parsed qview object.

Usage

## S3 method for class 'qview'
plot(x, type = c("plate_map", "intensity_heatmap", "replicate_scatter"), ...)

Arguments

x

A qview object returned by read_qview().

type

One of "plate_map", "intensity_heatmap", "replicate_scatter". Default "plate_map".

...

Unused; for S3 generic compatibility.

Details

"plate_map" – heat-coloured plate map, one cell per well, fill by well type (standard / negative / sample / control).
"intensity_heatmap" – per-analyte facet, fill by replicate-1 pixel intensity per well.
"replicate_scatter" – replicate 1 vs replicate 2 pixel intensity per analyte.

Requires the ggplot2 package (Suggested).

Value

A ggplot object.

Examples


path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path, verbose = FALSE)
plot(qv, type = "plate_map")
plot(qv, type = "replicate_scatter")

Print a Q-View object

Description

Compact summary of a parsed qview object: project / plate identifiers, analyte panel, well-group counts by type, and whether the embedded report carries quantitative concentrations or only qualitative pixel intensities.

Usage

## S3 method for class 'qview'
print(x, ...)

Arguments

x

A qview object returned by read_qview().

...

Ignored.

Value

x, invisibly.

Examples

qv <- read_qview(system.file("extdata", "example.Q-View",
                             package = "qviewparsR"), verbose = FALSE)
print(qv)

Print a qview_summary object

Description

Usage

## S3 method for class 'qview_summary'
print(x, ...)

Arguments

x

A qview_summary object returned by summary.qview().

...

Unused; for S3 generic compatibility.

Value

x, invisibly.

Examples

path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path, verbose = FALSE)
summary(qv)

Launch the qviewparsR Q-View Shiny app

Description

Usage

qview_app(max_upload_mb = 512, ...)

Arguments

max_upload_mb

Numeric. Maximum upload size per request, in megabytes. Q-View project files routinely exceed the Shiny upload default of 5 MB; this argument bumps the limit for the duration of the running app and restores the previous value on exit. Default 512 MB.

...

Forwarded to shiny::runApp().

Details

Interactive front-end for read_qview(). Uploads a .Q-View file (and optionally an accompanying well-assignment template CSV), displays the parsed metadata, analytes, well groups, and replicate tables, and lets the user download the parsed result as xlsx, rds, or a zip of per-table CSV files.

Requires the shiny, bslib, and DT packages (listed under Suggests).

Value

Invoked for its side effect of running the app.

Examples

if (interactive()) {
  qview_app()
}

Read a .Q-View project file

Description

Usage

read_qview(
  path,
  strip_prefix = FALSE,
  verbose = TRUE,
  call = rlang::caller_env()
)

Arguments

path

Character. Path to the .Q-View file.

strip_prefix

Logical. If TRUE, reverse Q-View's internal naming convention via strip_qview_prefix() so identifiers match the original well-assignment template. Default FALSE.

verbose

Logical. Print a short summary after parsing. Default TRUE.

call

The execution environment of the calling function. Used for error reporting; experts only.

Details

Parses a .Q-View binary container (a chemiluminescent multiplex ELISA project file holding an embedded H2 database plus binary LOB segments) and extracts the assay data: project metadata, analyte panel with units, well-group sample assignments, per-well replicate pixel intensities, summary statistics, and (when present) the embedded CSV report.

The file format is reverse-engineered from public binary inspection: it begins with a plain-text manifest, followed by three concatenated H2 database segments. The fully-formatted report Q-View renders for the user is stored as a CLOB inside the main H2 segment. This parser scans the binary for that CLOB, reassembles it across H2 page boundaries (2048-byte pages), and parses it as CSV.

Parsing is done in pure R: no Java runtime, no H2 database driver, no system dependencies beyond a working R installation.

Value

A list with class "qview" containing:

metadata: Named list: project, plate, image, imager, product, user, report_created, qview_version, template, container_version, file_path, parsed_at.
manifest: Tibble with one row per declared file entry (name, size_bytes, parent).
segments: Tibble of H2 segment byte ranges (segment, start, end, size).
analytes: Tibble: spot_number, analyte, unit, plus lod, lloq, uloq, assay_control_low, assay_control_high when reported.
well_groups: Tibble: well_group, sample_id, is_standard, is_negative, is_sample, is_control, well_type.
pixel_intensities: Long-format tibble of replicate readings: well_group, sample_id, well, replicate, analyte, unit, pixel_intensity, dilution.
summary_statistics: Long-format tibble of per-group averages, std-dev, and CV statistics: well_group, sample_id, statistic, analyte, value, unit.
concentrations: Long-format concentration tibble or NULL if the regression model is "Qualitative".
curve_fit: Tibble with analyte, regression_model, or NULL if not reported.
report_csv: Character vector of the raw CSV report lines, or NULL if no report was generated.
plate_layout: Tibble with one row per well: well, plate_row, plate_col, well_group, sample_id, well_type, dilution.

Examples

# A small synthetic .Q-View ships with the package:
path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path)
qv
qv$analytes
head(qv$pixel_intensities)

if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot(qv, type = "plate_map")
}

Read a Q-View report export (CSV or XLSX)

Description

Usage

read_qview_report(
  path,
  strip_prefix = FALSE,
  verbose = TRUE,
  call = rlang::caller_env()
)

Arguments

path

Character. Path to a Q-View report export (.csv or .xlsx).

strip_prefix

Logical. If TRUE, reverse Q-View's internal naming convention via strip_qview_prefix(). Default FALSE.

verbose

Logical. Print a short summary after parsing. Default TRUE.

call

The execution environment of the calling function. Used for error reporting; experts only.

Details

Parses one of the flat report files Q-View exports next to the native .Q-View container – the ..._auto_report or ..._auto_all-parameters_report export, as either .csv or .xlsx – and returns the same qview object read_qview() builds from the binary container. Use it when only the exports were kept and the original .Q-View project file is unavailable.

The export shares its report layout with the CLOB embedded in the binary container, so the two readers agree on concentrations and pixel intensities. Two behaviours differ from read_qview(), both to preserve information the study workflows rely on:

The plain "Reduced Concentration" point estimate (one row per sample, the value the exports headline) is captured with statistic == "reduced". read_qview() currently keeps only the per-replicate / summary concentration rows.
Out-of-range cells are preserved, not dropped: a "< 52.50" cell yields concentration = 52.50 with flag = "<", a "> 7700" cell flag = ">", and an "Incalculable ..." cell concentration = NA with flag = "incalculable". In-range cells carry flag = NA.

Value

A list with class "qview", structured as the read_qview() return value, with these deviations. Container-only slots (manifest, segments) are zero-row tibbles; metadata$container_version is NA. The concentrations tibble carries one extra column, flag (NA / "<" / ">" / "incalculable"), relative to read_qview(). report_csv echoes the full export in file order (metadata preamble, blank spacer rows, the analyte header, then the data rows), whereas read_qview()'s report_csv holds only the unique report data lines.

Examples

path <- system.file("extdata", "example-report.csv",
                    package = "qviewparsR")
if (nzchar(path)) {
  qv <- read_qview_report(path)
  qv$concentrations
}

Read a Q-View well-assignment template CSV

Description

Usage

read_qview_template(path, verbose = TRUE, call = rlang::caller_env())

Arguments

path

Path to the template file (csv).

verbose

Logical. Print a short summary after parsing. Default TRUE.

call

The execution environment of the calling function. Used for error reporting; experts only.

Details

Parses the plate-template CSV that Q-View imports for sample assignment. The file uses a multi-section layout: an NxM cell in the top-left declares the plate dimensions, followed by sections labelled ⁠Group Name⁠, ⁠Group Type⁠, and ⁠Dilution Factor⁠. Each section is one row per plate row and one column per plate column.

All template data is also embedded inside the .Q-View file itself (and is recovered by read_qview()); this function exists for setting up new plates or cross-validating Q-View imports against the original template.

Value

A tibble::tibble() with one row per well and columns well (character, e.g. "A1"), plate_row (character, "A"..), plate_col (integer), sample_id (character), group_type (character), dilution (numeric).

Examples

path <- system.file("extdata", "example-template.csv",
                    package = "qviewparsR")
layout <- read_qview_template(path)
head(layout)

Reverse the Q-View internal naming convention

Description

Usage

strip_qview_prefix(x)

Arguments

x

Character vector of Q-View internal names.

Details

On import, the producing software prefixes well-assignment template names with single-letter codes:

"Cal 1" ... "Cal N" -> "ICal 1" ... "ICal N" (Internal calibrator)
"Low" -> "GLow"
"High" -> "HHigh"
"FD..." and any all-digit ID -> "N..." (sample prefix)

strip_qview_prefix() reverses this transformation so that downstream code sees the identifiers exactly as they appear in the original template CSV. Strings that do not match a known prefix pattern are returned unchanged.

Value

Character vector of the same length as x, with prefixes stripped. NAs and unrecognised values pass through unchanged.

Examples

strip_qview_prefix(c("ICal 1", "GLow", "HHigh",
                     "NFD24277364", "N1211498458", "Plate 1"))

Summary statistics for a Q-View object

Description

Per-analyte mean, standard deviation, and coefficient of variation (sd / mean) of pixel intensities, by well-group type. Calibrator / standard wells are reported separately so calibration variability is easy to inspect.

Usage

## S3 method for class 'qview'
summary(object, ...)

Arguments

object

A qview object returned by read_qview().

...

Unused; for S3 generic compatibility.

Value

A tibble::tibble() with one row per well_type x analyte combination, columns: well_type, analyte, unit, n, mean, sd, cv, min, max.

Examples

path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path, verbose = FALSE)
summary(qv)

Convert plate row / column to a well label

Description

Usage

well_label(row, col, zero_based = FALSE)

Arguments

row

Integer or character. Either a 0/1-based row index or already a single letter ("A"...).

col

Integer column index (1-based or 0-based; values >= 1 are treated as 1-based).

zero_based

Logical. If TRUE, treat row and col as 0-based; if FALSE (default), treat them as 1-based.

Details

Converts 0-based or 1-based row and column indices to the standard "A1" ... "H12" plate notation. Vectorised.

Value

Character vector of well labels (e.g. "A1", "H12"), recycled to the longer of row / col.

Examples

well_label(0, 0, zero_based = TRUE)   # "A1"
well_label(7, 11, zero_based = TRUE)  # "H12"
well_label("C", 5)                    # "C5"

Write a Q-View object to disk

Description

Usage

write_qview_xlsx(
  qv,
  path,
  template = NULL,
  overwrite = FALSE,
  call = rlang::caller_env()
)

write_qview_csv(qv, path, template = NULL, call = rlang::caller_env())

write_qview_rds(qv, path, overwrite = FALSE, call = rlang::caller_env())

qview_to_xlsx(
  qv,
  path,
  template = NULL,
  overwrite = FALSE,
  call = rlang::caller_env()
)

qview_to_csv_dir(qv, dir, template = NULL, call = rlang::caller_env())

Arguments

qv

A qview object from read_qview().

path

Output path. For write_qview_xlsx() / write_qview_rds() this is a single file path; for write_qview_csv() it is the output directory (created if it does not exist).

template

Optional plate-template tibble (from read_qview_template()) to include as an extra sheet / file.

overwrite

Logical. If FALSE (the default), an existing destination triggers an error; set to TRUE to replace it. Ignored by write_qview_csv() (it only adds files).

call

The execution environment of the calling function. Used for error reporting; experts only.

dir

Deprecated alias for path accepted by qview_to_csv_dir(). Use path instead.

Details

Three writers, one for each common destination. All return the input qv invisibly so they compose with the pipe.

write_qview_xlsx() – one sheet per parsed table.
write_qview_csv() – one CSV per parsed table inside a directory.
write_qview_rds() – a single .rds containing the full qview object (lossless, the only round-trippable format).

Value

qv, invisibly, to support pipelines.

Examples

path <- system.file("extdata", "example.Q-View", package = "qviewparsR")
qv <- read_qview(path, verbose = FALSE)

out <- tempfile()
dir.create(out)
qv |>
  write_qview_rds(file.path(out, "plate.rds")) |>
  write_qview_csv(file.path(out, "plate_csv"))
list.files(out, recursive = TRUE)

Package {qviewparsR}

qviewparsR: Read .Q-View Multiplex ELISA Project Files

Description

Main functions

Author(s)

See Also

Coerce a Q-View object to a tibble

Description

Usage

Arguments

Value

See Also

Examples

Test whether an object is a qview

Description

Usage

Arguments

Value

See Also

Examples

Plot a Q-View object

Description

Usage

Arguments

Details

Value

See Also

Examples

Print a Q-View object

Description

Usage

Arguments

Value

See Also

Examples

Print a qview_summary object

Description

Usage

Arguments

Value

See Also

Examples

Launch the qviewparsR Q-View Shiny app

Description

Usage

Arguments

Details

Value

Examples

Read a .Q-View project file

Description

Usage

Arguments

Details

Value

See Also

Examples

Read a Q-View report export (CSV or XLSX)

Description

Usage

Arguments

Details

Value

See Also

Examples

Read a Q-View well-assignment template CSV

Description

Usage

Arguments

Details

Value

See Also

Examples

Reverse the Q-View internal naming convention

Description

Usage

Arguments

Details

Value

See Also

Test whether an object is a `qview`