In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Details

# small tools to make handling optional elements easier
maybeIncl <- function(cond, tag) if (cond) tag else NULL
callIncl <- function(f, ..., fixed = NULL) do.call(f, c(pruneList(list(...)), fixed))

doSelParent <- utils$hasComponentsTPs() && (settings$features$chromatograms$large || utils$hasComponentsFromTPs() ||
                                                settings$features$chromatograms$intensityPlots)

mdprintf("Generating report parts: ")

bslib::layout_column_wrap(
    id = "detailsLayout",
    width = 1,
    height = "100%",
    style = "padding-bottom: 10px; padding-right: 10px; grid-template-rows: 1fr 1fr;",
    bslib::card(
        full_screen = TRUE,
        bslib::card_header("Feature groups"),
        bsCardBodyNoFill(
            class = "mt-2",
            htmltools::withTags({
                callIncl(div, class = "pb-1",
                    label("for" = "view-select", "View"),
                    callIncl(select, name = "view", id = "view-select", onChange = "updateView(this.value)",
                           style = list("margin-right" = "10px", "margin-top" = " 3px"),
                           option(value = "Plain", "Plain"),
                           maybeIncl(utils$hasSuspects(), option(value = "Suspects", "Suspects")),
                           maybeIncl(utils$hasInternalStandards(), option(value = "ISTDs", "Internal standards")),
                           maybeIncl(utils$hasComponents(), option(value = "Components", "Components")),
                           maybeIncl(utils$hasComponentsTPs(), option(value = "TPs", "Transformation products"))
                    ),

                    input(type = "checkbox", id = "fg-cols-info", onChange = 'showFGCols("group", this.checked)',
                          checked = TRUE),
                    label("for" = "fg-cols-info", "Group info"),
                    input(type = "checkbox", id = "fg-cols-int", onChange = 'showFGCols("intensities", this.checked)',
                          checked = TRUE),
                    label("for" = "fg-cols-int", "Intensities"),
                    maybeIncl(utils$hasConcs(), input(type = "checkbox", id = "fg-cols-concs",
                                                      onChange = 'showFGCols("concentrations", this.checked)',
                                                      checked = TRUE)),
                    maybeIncl(utils$hasConcs(), label("for" = "fg-cols-concs", "Concentrations")),
                    maybeIncl(utils$hasFQualities(), input(type = "checkbox", id = "fg-cols-qual",
                                                           onChange = 'showFGCols("qualities", this.checked)')),
                    maybeIncl(utils$hasFQualities(), label("for" = "fg-cols-qual", "Quality scores")),
                    maybeIncl(settings$features$chromatograms$large, input(type = "checkbox", id = "fg-large-chroms",
                                                                  onChange = 'showFGCols("chrom_large", this.checked)')),
                    maybeIncl(settings$features$chromatograms$large, label("for" = "fg-large-chroms", "Large chromatograms")),
                    input(type = "checkbox", id = "fg-filter", onChange = 'toggleFGFilters(this.checked)'),
                    label("for" = "fg-filter", style = list("margin-right" = "10px"), "Filters"),

                    button(type = "button", class = "btn btn-primary btn-sm",
                           onClick = "downloadCSV(getSelFGTableElement(), 'featureGroups.csv')", "Download CSV"),
                    button(type = "button", class = "btn btn-primary btn-sm", id = "fg-expand",
                           onClick = "Reactable.toggleAllRowsExpanded(getSelFGTableElement())",
                           style = list(display = "none"), "Expand/collapse"),

                    div(class = "float-right",
                        label("for" = "fg-search", "Search"),
                        input(type = "text", id = "fg-search", oninput="Reactable.setSearch(getSelFGTableElement(), this.value)"),

                        div(class = "btn-group btn-group-sm mx-1", role = "group", "aria-label" = "ratio group",
                            input(type = "radio", class = "btn-check", name = "ratiobtn", id = "ratio21",
                                  autocomplete = "off", onChange = 'setDetailsRatio(2, 1)'),
                            label(class = "btn btn-outline-primary", "for" = "ratio21", "2:1"),
                            input(type = "radio", class = "btn-check", name = "ratiobtn", id = "ratio32",
                                  autocomplete = "off", onChange = 'setDetailsRatio(3, 2)'),
                            label(class = "btn btn-outline-primary", "for" = "ratio32", "3:2"),
                            input(type = "radio", class = "btn-check", name = "ratiobtn", id = "ratio11",
                                  autocomplete = "off", onChange = 'setDetailsRatio(1, 1)', checked = TRUE),
                            label(class = "btn btn-outline-primary", "for" = "ratio11", "1:1"),
                            input(type = "radio", class = "btn-check", name = "ratiobtn", id = "ratio23",
                                  autocomplete = "off", onChange = 'setDetailsRatio(2, 3)'),
                            label(class = "btn btn-outline-primary", "for" = "ratio23", "2:3"),
                            input(type = "radio", class = "btn-check", name = "ratiobtn", id = "ratio12",
                                  autocomplete = "off", onChange = 'setDetailsRatio(1, 2)'),
                            label(class = "btn btn-outline-primary", "for" = "ratio12", "1:2")
                        ),
                    )
                )
            })
        ),
        callIncl(bslib::card_body_fill,
            utils$genFGTablePlain(),
            maybeIncl(utils$hasSuspects(), utils$genFGTableSuspects()),
            maybeIncl(utils$hasInternalStandards(), utils$genFGTableISTDs()),
            maybeIncl(utils$hasComponents(), utils$genFGTableComponents()),
            maybeIncl(utils$hasComponentsTPs(), utils$genFGTableTPs())
        ),
    ),
    callIncl(bslib::layout_column_wrap,
        fixed = list(width = NULL),
        style = htmltools::css(grid_template_columns = "1fr 2fr"),
        heights_equal = "row",
        class = "bottomLayout",
        maybeIncl(utils$hasSuspects(), bslib::navs_tab_card(
            title = "Selected suspect",
            full_screen = TRUE,
            bslib::nav(
                "Suspect",
                bsCardBodyNoFill(
                    class = "propTabAndImg pt-2",
                    utils$genSuspInfoTable("suspInfoTab"),
                    htmltools::img(id = "struct_view-suspect", style = "min-width: 20%;")
                )
            ),
        )),
        maybeIncl(utils$hasInternalStandards(), bslib::navs_tab_card(
            title = "Selected internal standard",
            full_screen = TRUE,
            bslib::nav(
                "Internal standard",
                bsCardBodyNoFill(
                    class = "propTabAndImg pt-2",
                    utils$genISTDInfoTable(),
                    htmltools::img(id = "struct_view-istd", style = "min-width: 20%;")
                )
            ),
        )),
        maybeIncl(utils$hasComponents(), callIncl(bslib::navs_tab_card,
            title = "Selected component",
            full_screen = TRUE,
            bslib::nav(
                "Chromatogram",
                bslib::card_body_fill(htmltools::img(id = "chrom_view-component"))
            ),
            bslib::nav(
                "Spectrum",
                bslib::card_body_fill(htmltools::img(id = "spectrum_view-component"))
            ),
            maybeIncl(utils$hasComponentsIntClust(), bslib::nav(
                "Profile",
                bslib::card_body_fill(
                    htmltools::img(id = "profileRel_view-component"),
                    htmltools::img(id = "profileAbs_view-component")
                )
            )),
            maybeIncl(utils$hasComponentInfo(), bslib::nav(
                "Component info",
                bsCardBodyNoFill(
                    class = "pt-2",
                    utils$genComponentInfoTable(),
                )
            ))
        )),
        maybeIncl(doSelParent, callIncl(bslib::navs_tab_card,
            title = "Selected parent",
            full_screen = TRUE,
            maybeIncl(settings$features$chromatograms$large, bslib::nav(
                "Chromatogram",
                bslib::card_body_fill(htmltools::img(id = "chrom_view-tp"))
            )),
            maybeIncl(utils$hasComponentsFromTPs(), bslib::nav(
                "Suspects",
                bsCardBodyNoFill(class = "mx-auto", htmltools::strong("Parent")),
                bsCardBodyNoFill(
                    class = "propTabAndImg",
                    utils$genSuspInfoTable("parentInfoTab"),
                    htmltools::img(id = "struct_view-parent", style = "min-width: 20%;")
                ),
                bsCardBodyNoFill(class = "mx-auto", htmltools::strong("Transformation product")),
                bsCardBodyNoFill(
                    class = "propTabAndImg",
                    utils$genSuspInfoTable("TPInfoTab"),
                    htmltools::img(id = "struct_view-tp", style = "min-width: 20%;")
                )
            )),
            maybeIncl(settings$features$intensityPlots, bslib::nav(
                "Intensities",
                class = "mt-2",
                bslib::card_body_fill(htmltools::img(id = "int_plot-parent"))
            )),
            maybeIncl(utils$hasTPGraphs() && utils$hasComponentsFromTPs(), bslib::nav(
                "Transformations",
                bslib::card_body_fill(utils$genTPGraphs())
            ))
        )),
        callIncl(bslib::navs_tab_card,
            title = "Selected feature group",
            id = "fGroupSelTabs",
            full_screen = TRUE,
            bslib::nav(
                "Features",
                bsCardBodyNoFill(
                    class = "mt-2",
                    htmltools::withTags({
                        callIncl(div, class = "pb-1",
                            label("for" = "features-groupBy", "Group by"),
                            callIncl(select, id = "features-groupBy", onChange = "Reactable.setGroupBy('featuresTab', [ this.value ])",
                                     style = list("margin-right" = "10px", "margin-top" = " 3px"),
                                     option(value = "", "None"),
                                     option(value = "rGroup", "Replicate group"),
                                     maybeIncl(utils$hasSets(), option(value = "set", "Set"))
                            ),

                            maybeIncl(utils$hasFQualities(), input(type = "checkbox", id = "features-cols-qual",
                                                                   onChange = 'showFeatQualityCols(this.checked)')),
                            maybeIncl(utils$hasFQualities(), label("for" = "features-cols-qual", "Quality scores")),
                            input(type = "checkbox", id = "features-filter", onChange = 'toggleFeatFilters(this.checked)'),
                            label("for" = "features-filter", style = list("margin-right" = "10px"), "Filters"),

                            button(type = "button", class = "btn btn-primary btn-sm",
                                   onClick = "downloadCSV('featuresTab', 'features.csv')", "Download CSV"),
                            button(type = "button", class = "btn btn-primary btn-sm", id = "feat-expand",
                                   onClick = "Reactable.toggleAllRowsExpanded('featuresTab')", "Expand/collapse")
                        )
                    })
                ),
                bslib::card_body_fill(utils$genFeaturesTable())
            ),
            maybeIncl(utils$hasConcs(), bslib::nav(
                "Concentrations",
                bsCardBodyNoFill(
                    class = "mt-2",
                    htmltools::withTags({
                        div(class = "pb-1",
                            input(type = "checkbox", id = "concs-filter", onChange = 'toggleConcsFilters(this.checked)'),
                            label("for" = "concs-filter", style = list("margin-right" = "10px"), "Filters"),
                            button(type = "button", class = "btn btn-primary btn-sm",
                                   onClick = "downloadCSV('concsTab', 'concentrations.csv')", "Download CSV")
                        )
                    })
                ),
                bslib::card_body_fill(utils$genConcsTable())
            )),
            maybeIncl(utils$hasTox(), bslib::nav(
                "Toxicities",
                bsCardBodyNoFill(
                    class = "mt-2",
                    htmltools::withTags({
                        div(class = "pb-1",
                            input(type = "checkbox", id = "tox-filter", onChange = 'toggleToxFilters(this.checked)'),
                            label("for" = "tox-filter", style = list("margin-right" = "10px"), "Filters"),
                            button(type = "button", class = "btn btn-primary btn-sm",
                                   onClick = "downloadCSV('toxTab', 'toxicities.csv')", "Download CSV")
                        )
                    })
                ),
                bslib::card_body_fill(utils$genToxTable())
            )),
            maybeIncl(settings$features$intensityPlots, bslib::nav(
                "Intensities",
                class = "mt-2",
                bslib::card_body_fill(htmltools::img(id = "int_plot"))
            )),
            maybeIncl(utils$hasMSPL(), bslib::nav(
                "MS peak lists",
                callIncl(bsCardBodyNoFill,
                    style = "display: grid; grid-template-columns: 1fr 1fr; column-gap: 50px; justify-items:center;",
                    htmltools::strong("MS"),
                    htmltools::strong("MS/MS"),
                    maybeIncl(settings$MSPeakLists$spectra, htmltools::img(id = "spectrumMS", style = "min-width: 20%;")),
                    maybeIncl(settings$MSPeakLists$spectra, htmltools::img(id = "spectrumMSMS", style = "min-width: 20%;")),
                    utils$genMSPLTable(1),
                    utils$genMSPLTable(2)
                )
            )),
            maybeIncl(utils$hasFormulas(), bslib::nav(
                "Formulas",
                bsCardBodyNoFill(
                    class = "mt-2",
                    htmltools::withTags({
                        div(class = "pb-1",
                            input(type = "checkbox", id = "formulas-filter", onChange = 'toggleFormFilters(this.checked)'),
                            label("for" = "formulas-filter", style = list("margin-right" = "10px"), "Filters"),
                            input(type = "checkbox", id = "formulas-susp_only", onChange = 'toggleAnnOnlySusp("formulas", this.checked)'),
                            label("for" = "formulas-susp_only", "Suspect only"),
                            button(type = "button", class = "btn btn-primary btn-sm",
                                   onClick = "downloadCSV('formulasTab', 'formulas.csv')", "Download CSV"),
                            button(type = "button", class = "btn btn-primary btn-sm", id = "form-expand",
                                   onClick = "Reactable.toggleAllRowsExpanded('formulasTab')", "Expand/collapse"),
                        )
                    })
                ),
                bslib::card_body_fill(utils$genFormulasTable())
            )),
            maybeIncl(utils$hasCompounds(), bslib::nav(
                "Compounds",
                bsCardBodyNoFill(
                    class = "mt-2",
                    htmltools::withTags({
                        div(class = "pb-1",
                            label("for" = "compounds-groupBy", "Group by"),
                            select(id = "compounds-groupBy", onChange = "Reactable.setGroupBy('compoundsTab', [ this.value ])",
                                   style = list("margin-right" = "10px", "margin-top" = " 3px"),
                                   option(value = "", "None"),
                                   option(value = "neutral_formula", "Formula")
                            ),

                            input(type = "checkbox", id = "compounds-filter", onChange = 'toggleCompFilters(this.checked)'),
                            label("for" = "compounds-filter", "Filters"),
                            input(type = "checkbox", id = "compounds-susp_only", onChange = 'toggleAnnOnlySusp("compounds", this.checked)'),
                            label("for" = "compounds-susp_only", "Suspect only"),

                            button(type = "button", class = "btn btn-primary btn-sm ms-2",
                                   onClick = "downloadCSV('compoundsTab', 'compounds.csv')", "Download CSV"),
                            button(type = "button", class = "btn btn-primary btn-sm", id = "comp-expand",
                                   onClick = "Reactable.toggleAllRowsExpanded('compoundsTab')", "Expand/collapse"),

                            a(class = "ms-2", id = "openMF", target = "_blank", "MetFrag Web"),
                        )
                    })
                ),
                bslib::card_body_fill(utils$genCompoundsTable())
            )),
            maybeIncl(utils$hasCompsCluster(), bslib::nav(
                "Compounds clusters",
                bslib::card_body_fill(
                    htmltools::img(id = "comps_cluster-dendro"),
                    utils$genCompClustsImgs()
                )
            )),
            maybeIncl(utils$hasSuspAnn(), bslib::nav(
                "Suspect annotation",
                bslib::card_body_fill(
                    htmltools::div(style = "margin: 20px;", utils$genSuspAnnTable())
                )
            )),
            maybeIncl(utils$hasTPSims(), bslib::nav(
                "Parent similarity",
                bsCardBodyNoFill(
                    class = "parentSim",
                    utils$genTPSimTable(),
                    # hide img if image is unavailable: https://stackoverflow.com/a/22051972
                    htmltools::img(id = "similarity_spec", style = "display: none;",
                                   onerror = "this.style.display='none'")
                )
            ))
        )
    )
)

mdprintf("Done!\n")