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dash-info.yaml
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dash-info.yaml
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pkg_help_description: >-
A suite of components that makes 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
r_examples:
- name: dashbioAlignmentChart
dontrun: TRUE
code: |
library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(dashBio)
data(p53fasta)
app <- Dash$new()
app$layout(htmlDiv(list(
dashbioAlignmentChart(
id='my-dashbio-alignmentchart',
data=p53fasta
)
)
)
)
app$run_server(showcase = TRUE)
- name: dashbioAlignmentViewer
dontrun: TRUE
code: |
library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(dashBio)
data(p53fasta)
app <- Dash$new()
app$layout(htmlDiv(list(
dashbioAlignmentViewer(
id='my-dashbio-alignmentviewer',
data=p53fasta
)
)
)
)
app$run_server(showcase = TRUE)
- name: dashbioCircos
dontrun: TRUE
code: |
library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(dashBio)
app <- Dash$new()
pathToData <- system.file("extdata/circos_graph_data.json", package = "dashBio")
circos_graph_data <- jsonlite::fromJSON(pathToData, simplifyDataFrame=FALSE)
app$layout(htmlDiv(list(
dashbioCircos(
id = 'my-dashbio-circos',
tracks = list(
list('type' = 'CHORDS',
'data' = circos_graph_data[['chords']],
'opacity' = '0.7',
'color' = list('name' = 'color'),
'config' = list(
'tooltipContent' = list(
'source' = 'source',
'sourceID' = 'id',
'target' = 'target',
'targetID' = 'id',
'targetEnd' = 'end'
)
)
)),
layout = circos_graph_data[['GRCh37']]
)
)
)
)
app$run_server(showcase = TRUE)
- name: dashbioIdeogram
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
app <- Dash$new()
app$layout(
htmlDiv(
list(
htmlLabel("Click a chromosome for a closer look; double-click to return to the overview:"),
dashbioIdeogram(
id='my-dashbio-ideogram',
chrHeight=250
)
),
style = list("text-align" = "center")
)
)
app$run_server()
- name: dashbioManhattan
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
app <- Dash$new()
app$layout(
htmlDiv(
list(
dccGraph(id = 'manhattan-plot',
figure = dashbioManhattan(HapMap,
snp = "SNP",
highlight = significantSNP)
)
)
)
)
app$run_server()
- name: dashbioMolecule2dViewer
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
library(jsonlite)
# data available within the package:
pathToModelData <- system.file("extdata/mol2d_buckminsterfullerene.json", package = "dashBio")
modelData <- jsonlite::read_json(pathToModelData)
app <- Dash$new()
app$layout(
htmlDiv(
list(
htmlLabel("Click and drag an element to rotate the molecule in 2D space:"),
dashbioMolecule2dViewer(
id = 'my-dashbio-molecule2d',
modelData = modelData
)
),
style = list("text-align" = "center",
"border-style" = "solid")
)
)
app$run_server()
- name: dashbioMolecule3dViewer
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
library(jsonlite)
# data available within the package:
pathToModelData <- system.file("extdata/model_data.json", package = "dashBio")
pathToStylesData <- system.file("extdata/styles_data.json", package = "dashBio")
modelData <- jsonlite::read_json(pathToModelData)
stylesData <- jsonlite::read_json(pathToStylesData)
app <- Dash$new()
app$layout(
htmlDiv(
list(
htmlLabel("Click and drag to rotate the molecule in 3D space:"),
dashbioMolecule3dViewer(
id = 'my-dashbio-molecule3d',
styles = stylesData,
modelData = modelData,
selectionType = 'Chain',
backgroundColor='#FF0000',
backgroundOpacity=0.2
)
),
style = list("text-align" = "center",
"border-style" = "solid")
)
)
app$run_server()
- name: dashbioNeedlePlot
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
pathToData <- system.file("extdata/needle_PIK3CA.json", package="dashBio")
mdata <- jsonlite::read_json(pathToData)
app <- Dash$new()
app$layout(
htmlDiv(
list(
dashbioNeedlePlot(
id = 'my-dashbio-needleplot',
mutationData = mdata
)
)
)
)
app$run_server()
- name: dashbioOncoPrint
dontrun: TRUE
code: |
library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(dashBio)
app <- Dash$new()
pathToData <- system.file("extdata/cBioPortalData.json", package = "dashBio")
cBioPortalData <- jsonlite::fromJSON(pathToData, simplifyDataFrame=FALSE)
app$layout(htmlDiv(list(
dashbioOncoPrint(
id = 'my-dashbio-oncoprint',
data = cBioPortalData
)
)
)
)
app$run_server(showcase = TRUE)
- name: dashbioSequenceViewer
dontrun: TRUE
code: |
library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(dashBio)
app <- Dash$new()
app$layout(htmlDiv(list(
dashbioSequenceViewer(
id = 'my-dashbio-sequenceviewer',
sequence = "MALIPDLAMETWLLLAVSLVLLYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGA"
)
)
)
)
app$run_server(showcase = TRUE)
- name: dashbioSpeck
dontrun: TRUE
code: |
library(dash)
library(dashHtmlComponents)
library(dashCoreComponents)
library(dashBio)
app <- Dash$new()
# a helper function to simplify data import
importSpeck <- function(filepath,
header = FALSE,
skip = 2) {
textdata <- read.table(
text = paste0(
readLines(filepath), collapse="\n"
),
header = header,
skip = skip,
col.names = c("symbol", "x", "y", "z"),
stringsAsFactors = FALSE)
return(dashTable::df_to_list(textdata))
}
# data available within the package:
caffeine <- importSpeck(system.file("extdata/caffeine.xyz",
package = "dashBio"))
methane <- importSpeck(system.file("extdata/methane.xyz",
package = "dashBio"))
testosterone <- importSpeck(system.file("extdata/testosterone.xyz",
package = "dashBio"))
app$layout(htmlDiv(list(
htmlDiv(list(
htmlDiv(
id = 'speck-container',
children = list(
dashbioSpeck(
id = 'speck',
view = list('resolution' = 600, 'zoom'= 0.1),
scrollZoom = TRUE
)
),
style = list('display' = 'inline-block')
),
htmlDiv(list(
htmlLabel("Select a molecule to render:"),
dccDropdown(id = 'molecule-dropdown',
value = 'caffeine',
disabled = FALSE,
multi = FALSE,
options = list(list(value = "caffeine", label = "Caffeine"),
list(value = "methane", label = "Methane"),
list(value = "testosterone", label = "Testosterone")))
),
style = list('display' = 'inline-block',
'position' = 'absolute',
'top' = '25px',
'right' = '50px',
'width' = '300px',
'padding' = '10px'),
id = 'selector'
)
),
style = list('width' = '80\%',
'display' = 'inline-block')
)
)
)
)
app$callback(output=list(id='speck', property='data'),
params=list(
input(id='molecule-dropdown', property='value')),
function(molecule)
{
if (molecule == "caffeine") caffeine
else if (molecule == "methane") methane
else if (molecule == "testosterone") testosterone
}
)
app$run_server()
- name: dashbioVolcano
dontrun: TRUE
code: |
library(dash)
library(dashBio)
library(dashHtmlComponents)
library(dashCoreComponents)
app <- Dash$new()
data(voldata)
app$layout(
htmlDiv(
list(
'Effect sizes',
dccRangeSlider(
id = 'volcanoplot-input',
min = -3,
max = 3,
step = 0.05,
marks = setNames(
lapply(-3:3,
function(i){
list(label = as.character(i))
}),
-3:3
),
value = c(-0.5, 1)
),
htmlBr(),
htmlDiv(
dccGraph(
id = 'my-dashbio-volcanoplot',
figure = dashbioVolcano(
dataframe = voldata
)
)
)
)
)
)
app$callback(
output = list(id = 'my-dashbio-volcanoplot', property = 'figure'),
params = list(input(id = 'volcanoplot-input', property = 'value')),
function(effects) {
dashbioVolcano(
dataframe = voldata,
genomewideline_value = 2.5,
effect_size_line = unlist(effects),
)
}
)
app$run_server()