Update dashBio package for compatibility with dash 0.1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dashBio
 Title: Dash components for bioinformatics
-Version: 0.0.11
+Version: 0.1.2
 Authors @R: as.person(c(The Plotly Team <dashbio@plot.ly>))
 Description: Dash components for bioinformatics
 Depends: R (>= 3.0.2), manhattanly
@@ -12,4 +12,4 @@ BugReports: https://github.com/plotly/dash-bio/issues
 Encoding: UTF-8
 LazyData: true
 Author: The Plotly Team [aut]
-Maintainer: The Plotly Team <dashbio@plot.ly>
+Maintainer: Ryan Patrick Kyle <ryan@plot.ly>

NAMESPACE

@@ -4,6 +4,7 @@ export(dashbioAlignmentChart)
 export(dashbioAlignmentViewer)
 export(dashbioCircos)
 export(dashbioIdeogram)
+export(dashbioMolecule2dViewer)
 export(dashbioMolecule3dViewer)
 export(dashbioNeedlePlot)
 export(dashbioOncoPrint)
@@ -12,3 +13,5 @@ export(dashbioSpeck)
 export(dashbioManhattan)
 export(dashbioVolcano)
 import(manhattanly)
+
+import(dash)

R/dashbioAlignmentChart.R

@@ -2,16 +2,17 @@
 
 dashbioAlignmentChart <- function(id=NULL, eventDatum=NULL, data=NULL, extension=NULL, colorscale=NULL, opacity=NULL, textcolor=NULL, textsize=NULL, showlabel=NULL, showid=NULL, showconservation=NULL, conservationcolor=NULL, conservationcolorscale=NULL, conservationopacity=NULL, conservationmethod=NULL, correctgap=NULL, showgap=NULL, gapcolor=NULL, gapcolorscale=NULL, gapopacity=NULL, groupbars=NULL, showconsensus=NULL, tilewidth=NULL, tileheight=NULL, overview=NULL, numtiles=NULL, scrollskip=NULL, tickstart=NULL, ticksteps=NULL, width=NULL, height=NULL) {
 
+    props <- list(id=id, eventDatum=eventDatum, data=data, extension=extension, colorscale=colorscale, opacity=opacity, textcolor=textcolor, textsize=textsize, showlabel=showlabel, showid=showid, showconservation=showconservation, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationopacity=conservationopacity, conservationmethod=conservationmethod, correctgap=correctgap, showgap=showgap, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, showconsensus=showconsensus, tilewidth=tilewidth, tileheight=tileheight, overview=overview, numtiles=numtiles, scrollskip=scrollskip, tickstart=tickstart, ticksteps=ticksteps, width=width, height=height)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, eventDatum=eventDatum, data=data, extension=extension, colorscale=colorscale, opacity=opacity, textcolor=textcolor, textsize=textsize, showlabel=showlabel, showid=showid, showconservation=showconservation, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationopacity=conservationopacity, conservationmethod=conservationmethod, correctgap=correctgap, showgap=showgap, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, showconsensus=showconsensus, tilewidth=tilewidth, tileheight=tileheight, overview=overview, numtiles=numtiles, scrollskip=scrollskip, tickstart=tickstart, ticksteps=ticksteps, width=width, height=height),
+        props = props,
         type = 'AlignmentChart',
         namespace = 'dash_bio',
         propNames = c('id', 'eventDatum', 'data', 'extension', 'colorscale', 'opacity', 'textcolor', 'textsize', 'showlabel', 'showid', 'showconservation', 'conservationcolor', 'conservationcolorscale', 'conservationopacity', 'conservationmethod', 'correctgap', 'showgap', 'gapcolor', 'gapcolorscale', 'gapopacity', 'groupbars', 'showconsensus', 'tilewidth', 'tileheight', 'overview', 'numtiles', 'scrollskip', 'tickstart', 'ticksteps', 'width', 'height'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioAlignmentViewer.R

@@ -2,16 +2,17 @@
 
 dashbioAlignmentViewer <- function(id=NULL, eventDatum=NULL, data=NULL, extension=NULL, colorscale=NULL, opacity=NULL, textcolor=NULL, textsize=NULL, showlabel=NULL, showid=NULL, showconservation=NULL, conservationcolor=NULL, conservationcolorscale=NULL, conservationopacity=NULL, conservationmethod=NULL, correctgap=NULL, showgap=NULL, gapcolor=NULL, gapcolorscale=NULL, gapopacity=NULL, groupbars=NULL, showconsensus=NULL, tilewidth=NULL, tileheight=NULL, overview=NULL, numtiles=NULL, scrollskip=NULL, tickstart=NULL, ticksteps=NULL, width=NULL, height=NULL) {
 
+    props <- list(id=id, eventDatum=eventDatum, data=data, extension=extension, colorscale=colorscale, opacity=opacity, textcolor=textcolor, textsize=textsize, showlabel=showlabel, showid=showid, showconservation=showconservation, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationopacity=conservationopacity, conservationmethod=conservationmethod, correctgap=correctgap, showgap=showgap, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, showconsensus=showconsensus, tilewidth=tilewidth, tileheight=tileheight, overview=overview, numtiles=numtiles, scrollskip=scrollskip, tickstart=tickstart, ticksteps=ticksteps, width=width, height=height)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, eventDatum=eventDatum, data=data, extension=extension, colorscale=colorscale, opacity=opacity, textcolor=textcolor, textsize=textsize, showlabel=showlabel, showid=showid, showconservation=showconservation, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationopacity=conservationopacity, conservationmethod=conservationmethod, correctgap=correctgap, showgap=showgap, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, showconsensus=showconsensus, tilewidth=tilewidth, tileheight=tileheight, overview=overview, numtiles=numtiles, scrollskip=scrollskip, tickstart=tickstart, ticksteps=ticksteps, width=width, height=height),
+        props = props,
         type = 'AlignmentViewer',
         namespace = 'dash_bio',
         propNames = c('id', 'eventDatum', 'data', 'extension', 'colorscale', 'opacity', 'textcolor', 'textsize', 'showlabel', 'showid', 'showconservation', 'conservationcolor', 'conservationcolorscale', 'conservationopacity', 'conservationmethod', 'correctgap', 'showgap', 'gapcolor', 'gapcolorscale', 'gapopacity', 'groupbars', 'showconsensus', 'tilewidth', 'tileheight', 'overview', 'numtiles', 'scrollskip', 'tickstart', 'ticksteps', 'width', 'height'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioCircos.R

@@ -2,16 +2,17 @@
 
 dashbioCircos <- function(enableDownloadSVG=NULL, enableZoomPan=NULL, id=NULL, style=NULL, eventDatum=NULL, selectEvent=NULL, layout=NULL, config=NULL, size=NULL, tracks=NULL) {
 
+    props <- list(enableDownloadSVG=enableDownloadSVG, enableZoomPan=enableZoomPan, id=id, style=style, eventDatum=eventDatum, selectEvent=selectEvent, layout=layout, config=config, size=size, tracks=tracks)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(enableDownloadSVG=enableDownloadSVG, enableZoomPan=enableZoomPan, id=id, style=style, eventDatum=eventDatum, selectEvent=selectEvent, layout=layout, config=config, size=size, tracks=tracks),
+        props = props,
         type = 'Circos',
         namespace = 'dash_bio',
         propNames = c('enableDownloadSVG', 'enableZoomPan', 'id', 'style', 'eventDatum', 'selectEvent', 'layout', 'config', 'size', 'tracks'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioIdeogram.R

@@ -2,16 +2,17 @@
 
 dashbioIdeogram <- function(id=NULL, style=NULL, className=NULL, annotationsLayout=NULL, annotations=NULL, annotationsPath=NULL, annotationsData=NULL, annotationTracks=NULL, annotationHeight=NULL, annotationsColor=NULL, histogramScaling=NULL, barWidth=NULL, showAnnotTooltip=NULL, assembly=NULL, brush=NULL, brushData=NULL, container=NULL, chrHeight=NULL, chrMargin=NULL, chrWidth=NULL, chromosomes=NULL, dataDir=NULL, organism=NULL, localOrganism=NULL, homology=NULL, perspective=NULL, fullChromosomeLabels=NULL, resolution=NULL, filterable=NULL, orientation=NULL, ploidy=NULL, ploidyDesc=NULL, ancestors=NULL, rangeSet=NULL, rotatable=NULL, rotated=NULL, sex=NULL, showChromosomeLabels=NULL, showBandLabels=NULL, showFullyBanded=NULL, showNonNuclearChromosomes=NULL) {
 
+    props <- list(id=id, style=style, className=className, annotationsLayout=annotationsLayout, annotations=annotations, annotationsPath=annotationsPath, annotationsData=annotationsData, annotationTracks=annotationTracks, annotationHeight=annotationHeight, annotationsColor=annotationsColor, histogramScaling=histogramScaling, barWidth=barWidth, showAnnotTooltip=showAnnotTooltip, assembly=assembly, brush=brush, brushData=brushData, container=container, chrHeight=chrHeight, chrMargin=chrMargin, chrWidth=chrWidth, chromosomes=chromosomes, dataDir=dataDir, organism=organism, localOrganism=localOrganism, homology=homology, perspective=perspective, fullChromosomeLabels=fullChromosomeLabels, resolution=resolution, filterable=filterable, orientation=orientation, ploidy=ploidy, ploidyDesc=ploidyDesc, ancestors=ancestors, rangeSet=rangeSet, rotatable=rotatable, rotated=rotated, sex=sex, showChromosomeLabels=showChromosomeLabels, showBandLabels=showBandLabels, showFullyBanded=showFullyBanded, showNonNuclearChromosomes=showNonNuclearChromosomes)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, style=style, className=className, annotationsLayout=annotationsLayout, annotations=annotations, annotationsPath=annotationsPath, annotationsData=annotationsData, annotationTracks=annotationTracks, annotationHeight=annotationHeight, annotationsColor=annotationsColor, histogramScaling=histogramScaling, barWidth=barWidth, showAnnotTooltip=showAnnotTooltip, assembly=assembly, brush=brush, brushData=brushData, container=container, chrHeight=chrHeight, chrMargin=chrMargin, chrWidth=chrWidth, chromosomes=chromosomes, dataDir=dataDir, organism=organism, localOrganism=localOrganism, homology=homology, perspective=perspective, fullChromosomeLabels=fullChromosomeLabels, resolution=resolution, filterable=filterable, orientation=orientation, ploidy=ploidy, ploidyDesc=ploidyDesc, ancestors=ancestors, rangeSet=rangeSet, rotatable=rotatable, rotated=rotated, sex=sex, showChromosomeLabels=showChromosomeLabels, showBandLabels=showBandLabels, showFullyBanded=showFullyBanded, showNonNuclearChromosomes=showNonNuclearChromosomes),
+        props = props,
         type = 'Ideogram',
         namespace = 'dash_bio',
         propNames = c('id', 'style', 'className', 'annotationsLayout', 'annotations', 'annotationsPath', 'annotationsData', 'annotationTracks', 'annotationHeight', 'annotationsColor', 'histogramScaling', 'barWidth', 'showAnnotTooltip', 'assembly', 'brush', 'brushData', 'container', 'chrHeight', 'chrMargin', 'chrWidth', 'chromosomes', 'dataDir', 'organism', 'localOrganism', 'homology', 'perspective', 'fullChromosomeLabels', 'resolution', 'filterable', 'orientation', 'ploidy', 'ploidyDesc', 'ancestors', 'rangeSet', 'rotatable', 'rotated', 'sex', 'showChromosomeLabels', 'showBandLabels', 'showFullyBanded', 'showNonNuclearChromosomes'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioMolecule2dViewer.R

@@ -0,0 +1,18 @@
+# AUTO GENERATED FILE - DO NOT EDIT
+
+dashbioMolecule2dViewer <- function(id=NULL, selectedAtomIds=NULL, width=NULL, height=NULL, modelData=NULL) {
+
+    props <- list(id=id, selectedAtomIds=selectedAtomIds, width=width, height=height, modelData=modelData)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
+    component <- list(
+        props = props,
+        type = 'Molecule2dViewer',
+        namespace = 'dash_bio',
+        propNames = c('id', 'selectedAtomIds', 'width', 'height', 'modelData'),
+        package = 'dashBio'
+        )
+
+    structure(component, class = c('dash_component', 'list'))
+}

R/dashbioMolecule3dViewer.R

@@ -2,16 +2,17 @@
 
 dashbioMolecule3dViewer <- function(id=NULL, selectionType=NULL, backgroundColor=NULL, backgroundOpacity=NULL, styles=NULL, modelData=NULL, atomLabelsShown=NULL, selectedAtomIds=NULL, labels=NULL, onRenderNewData=NULL, onChangeSelection=NULL) {
 
+    props <- list(id=id, selectionType=selectionType, backgroundColor=backgroundColor, backgroundOpacity=backgroundOpacity, styles=styles, modelData=modelData, atomLabelsShown=atomLabelsShown, selectedAtomIds=selectedAtomIds, labels=labels, onRenderNewData=onRenderNewData, onChangeSelection=onChangeSelection)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, selectionType=selectionType, backgroundColor=backgroundColor, backgroundOpacity=backgroundOpacity, styles=styles, modelData=modelData, atomLabelsShown=atomLabelsShown, selectedAtomIds=selectedAtomIds, labels=labels, onRenderNewData=onRenderNewData, onChangeSelection=onChangeSelection),
+        props = props,
         type = 'Molecule3dViewer',
         namespace = 'dash_bio',
         propNames = c('id', 'selectionType', 'backgroundColor', 'backgroundOpacity', 'styles', 'modelData', 'atomLabelsShown', 'selectedAtomIds', 'labels', 'onRenderNewData', 'onChangeSelection'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioNeedlePlot.R

@@ -2,16 +2,17 @@
 
 dashbioNeedlePlot <- function(id=NULL, mutationData=NULL, xlabel=NULL, ylabel=NULL, rangeSlider=NULL, needleStyle=NULL, domainStyle=NULL) {
 
+    props <- list(id=id, mutationData=mutationData, xlabel=xlabel, ylabel=ylabel, rangeSlider=rangeSlider, needleStyle=needleStyle, domainStyle=domainStyle)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, mutationData=mutationData, xlabel=xlabel, ylabel=ylabel, rangeSlider=rangeSlider, needleStyle=needleStyle, domainStyle=domainStyle),
+        props = props,
         type = 'NeedlePlot',
         namespace = 'dash_bio',
         propNames = c('id', 'mutationData', 'xlabel', 'ylabel', 'rangeSlider', 'needleStyle', 'domainStyle'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioOncoPrint.R

@@ -2,16 +2,17 @@
 
 dashbioOncoPrint <- function(id=NULL, eventDatum=NULL, data=NULL, padding=NULL, colorscale=NULL, backgroundcolor=NULL, range=NULL, showlegend=NULL, showoverview=NULL, width=NULL, height=NULL) {
 
+    props <- list(id=id, eventDatum=eventDatum, data=data, padding=padding, colorscale=colorscale, backgroundcolor=backgroundcolor, range=range, showlegend=showlegend, showoverview=showoverview, width=width, height=height)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, eventDatum=eventDatum, data=data, padding=padding, colorscale=colorscale, backgroundcolor=backgroundcolor, range=range, showlegend=showlegend, showoverview=showoverview, width=width, height=height),
+        props = props,
         type = 'OncoPrint',
         namespace = 'dash_bio',
         propNames = c('id', 'eventDatum', 'data', 'padding', 'colorscale', 'backgroundcolor', 'range', 'showlegend', 'showoverview', 'width', 'height'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioSequenceViewer.R

@@ -2,16 +2,17 @@
 
 dashbioSequenceViewer <- function(id=NULL, sequence=NULL, showLineNumbers=NULL, wrapAminoAcids=NULL, charsPerLine=NULL, toolbar=NULL, search=NULL, title=NULL, sequenceMaxHeight=NULL, badge=NULL, selection=NULL, coverage=NULL, legend=NULL, coverageClicked=NULL, mouseSelection=NULL, subpartSelected=NULL) {
 
+    props <- list(id=id, sequence=sequence, showLineNumbers=showLineNumbers, wrapAminoAcids=wrapAminoAcids, charsPerLine=charsPerLine, toolbar=toolbar, search=search, title=title, sequenceMaxHeight=sequenceMaxHeight, badge=badge, selection=selection, coverage=coverage, legend=legend, coverageClicked=coverageClicked, mouseSelection=mouseSelection, subpartSelected=subpartSelected)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, sequence=sequence, showLineNumbers=showLineNumbers, wrapAminoAcids=wrapAminoAcids, charsPerLine=charsPerLine, toolbar=toolbar, search=search, title=title, sequenceMaxHeight=sequenceMaxHeight, badge=badge, selection=selection, coverage=coverage, legend=legend, coverageClicked=coverageClicked, mouseSelection=mouseSelection, subpartSelected=subpartSelected),
+        props = props,
         type = 'SequenceViewer',
         namespace = 'dash_bio',
         propNames = c('id', 'sequence', 'showLineNumbers', 'wrapAminoAcids', 'charsPerLine', 'toolbar', 'search', 'title', 'sequenceMaxHeight', 'badge', 'selection', 'coverage', 'legend', 'coverageClicked', 'mouseSelection', 'subpartSelected'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/dashbioSpeck.R

@@ -2,16 +2,17 @@
 
 dashbioSpeck <- function(id=NULL, data=NULL, scrollZoom=NULL, view=NULL, presetView=NULL) {
 
+    props <- list(id=id, data=data, scrollZoom=scrollZoom, view=view, presetView=presetView)
+    if (length(props) > 0) {
+        props <- props[!vapply(props, is.null, logical(1))]
+    }
     component <- list(
-        props = list(id=id, data=data, scrollZoom=scrollZoom, view=view, presetView=presetView),
+        props = props,
         type = 'Speck',
         namespace = 'dash_bio',
         propNames = c('id', 'data', 'scrollZoom', 'view', 'presetView'),
         package = 'dashBio'
         )
 
-    component$props <- filter_null(component$props)
-
     structure(component, class = c('dash_component', 'list'))
 }
-

R/internal.R

@@ -1,10 +1,26 @@
 .dashBio_js_metadata <- function() {
 deps_metadata <- list(`dash_bio` = structure(list(name = "dash_bio",
-version = "0.0.11", src = list(href = NULL,
+version = "0.1.2", src = list(href = NULL,
 file = "deps"), meta = NULL,
-script = "bundle.js",
+script = 'bundle.js',
 stylesheet = NULL, head = NULL, attachment = NULL, package = "dashBio",
 all_files = FALSE), class = "html_dependency"))
 return(deps_metadata)
 }
 
+dash_assert_valid_wildcards <- function (attrib = list("data", "aria"), ...)
+{
+    args <- list(...)
+    validation_results <- lapply(names(args), function(x) {
+        grepl(paste0("^", attrib, "-[a-zA-Z0-9]{1,}$", collapse = "|"),
+            x)
+    })
+    if (FALSE %in% validation_results) {
+        stop(sprintf("The following wildcards are not currently valid in Dash: '%s'",
+            paste(names(args)[grepl(FALSE, unlist(validation_results))],
+                collapse = ", ")), call. = FALSE)
+    }
+    else {
+        return(args)
+    }
+}

dash-info.yaml

@@ -0,0 +1,4 @@
+pkg_help_description: >
+    Dash Bio is a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.
+pkg_help_title: >
+    Open-source Bioinformatics Components for Dash