-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathui.R
258 lines (244 loc) · 11.6 KB
/
ui.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
# DNAlandscapeR UI #
source("global.R")
shinyUI(navbarPage(HTML("<img src='harvard-logo.png'/>"),
## Consider adding the git hash again
tabPanel("Visualize",
tags$head(tags$style(HTML(mycss))),
tags$head(HTML("<script>
var _prum = [['id', '58390712724e3adfc3ac739a'],
['mark', 'firstbyte', (new Date()).getTime()]];
(function() {
var s = document.getElementsByTagName('script')[0]
, p = document.createElement('script');
p.async = 'async';
p.src = '//rum-static.pingdom.net/prum.min.js';
s.parentNode.insertBefore(p, s);
})();
</script>")),
headerPanel(fluidRow(column(6, tags$h1(tags$b('DNA Landscape'))),
tags$h4(column(6, tags$h3(textOutput("topText")))))),
sidebarLayout(
sidebarPanel(
uiOutput("trackoptions"),
tags$hr(),
tagAppendAttributes( # allows you to hit enter
textInput("ucscCoord", HTML("<h4><b>Select Region Coordinates</b></h4>"), value = ucsc_coord),
`data-proxy-click` = "plot.region2"
),
actionButton("plot.region2", "Plot Region", style='padding:10px; font-size:80%'),
tags$br(),tags$hr(),
uiOutput("plotGeneName"),
actionButton("plot.gene", "Plot Gene", style='padding:10px; font-size:80%'),
tags$br(),
tags$hr(),
actionButton("zoom.in", "Zoom In", style='padding:10px; font-size:80%'),
actionButton("zoom.out", "Zoom Out", style='padding:10px; font-size:80%'),
actionButton("clear", "Clear", style='padding:10px; font-size:80%'),
tags$br(),
tags$br(),
actionButton("left.big", HTML(" << "), style='padding:10px; font-size:80%'),
actionButton("left.small", HTML(" < "), style='padding:10px; font-size:80%'),
actionButton("right.small", HTML(" > "), style='padding:10px; font-size:80%'),
actionButton("right.big", HTML(" >> "), style='padding:10px; font-size:80%'),
#tags$hr(),
#fileInput("skipRegions", HTML("<h4><b>Jump through Regions</b></h4>"), multiple = FALSE, accept = NULL, width = NULL),
#actionButton("left.skip", "<<<", style='padding:10px; font-size:100%'),
#actionButton("right.skip", ">>>", style='padding:10px; font-size:100%'),
tags$hr(),
uiOutput("ucscGo"),
tags$br(),
downloadButton("downQuick", "Download Plot"), tags$br(), tags$br(),
conditionalPanel(condition="input.initializeExample==0", uiOutput("initExamp")),
tags$hr()),
mainPanel(
#div(id = "plot-container",
# tags$img(src = "spinner.gif", id = "loading-spinner"),
plotOutput("plot", dblclick = "plot_dblclick",brush = "plot_brush")
#)
),
fluid = TRUE
),
bsCollapse(id = "collapseAdvancedPlotOptions", open = c("Panel1", "Panel2", "Panel3"), multiple = TRUE,
bsCollapsePanel(title = HTML("<h4><b>Advanced Options</b></h4>"), value = "Panel1",
fluidRow(
column(4, radioButtons("organism", HTML("<h3><b>Specify Organism</b></h3>"),
choices = list("Human" = 1, "Mouse" = 2), selected = 1), tags$br(),
selectInput("showgenes", label=HTML("<h4><b>Genome Annotation</b></h4>"),
choices = list("Gene Bodies" = 1, "Detailed Gene Annotation" = 2, "None" = 0), selected = 1)
),
column(4,
sliderInput("smoother", HTML("<h3><b>Smooth Epigenetic Peaks<br></b></h3>
<h4><b>Window Size</b></h4>"), min=0, max=5000, value=500, step=50),
selectInput("FUN", label=HTML("<h4><b>Function to Smooth</b></h4>"),
choices = list("Mean"="mean", "Max"="max", "Median"="median"), selected = "mean"),
checkboxInput("methylSmooth", "Also smooth WGBS Tracks", value = TRUE, width = NULL),
checkboxInput("log2BW", "Log Transform Continuous Tracks", value = FALSE, width = NULL)
),
column(4, HTML("<h3><b>Track Customization</b></h3>"),tags$br(),
uiOutput("flipMe"), tags$br(),tags$br(),
uiOutput("showGenomeAnnotation")
)
),
tags$hr(),
fluidRow(
column(4, textInput3("chr", HTML("<h5><b>Chr </b></h5>"), value = default_chr)),
column(4, textInput3("start", HTML("<h5><b>Start </b></h5>"), value = default_start)),
column(4, textInput3("stop", HTML("<h5><b>Stop </b></h5>"), value = default_end))),tags$hr(),
actionButton("plot.region", "Plot Region"),
style = "default"),
bsCollapsePanel(title = HTML("<h4><b>ChIA-PET Tracks Configuration</b></h4>"), value = "Panel2",
fluidRow(
column(4,HTML("<h4><b>Individual Sample PET Cutoff</b></h4>"),
uiOutput("petThresholds")),
column(4, HTML("<h4><b>Configure ChIA-PET Visualization </b></h4>"),
checkboxInput("colorLoops", "Color Loops Based on Biological Annotation", value = TRUE, width = NULL),
checkboxInput("showSingleAnchors", "Show Single Anchors in ChIA-PET Tracks", value = FALSE, width = NULL)),
column(4, selectInput("loopWidthNorm", label=HTML("<h4><b>ChIA-PET Loop Width Normalization</b></h4>"),
choices = list("Between Track" = 1, "Within Track" = 2, "None" = 0), selected = 1))),
tags$hr(),
actionButton("refresh2", "Refresh Plot"),
style = "default"),
bsCollapsePanel(title = HTML("<h4><b>Hi-C Tracks Configuration</b></h4>"), value = "Panel3",
fluidRow(
column(4,HTML("<h4><b>Individual Sample Resolution</b></h4>"),
uiOutput("HiCresolutions")),
column(4, HTML("<h4><b>Configure Hi-C Data</b></h4>"),
checkboxInput("showlegend", "Show Legend on Plots", value = TRUE, width = NULL),
radioButtons("HiCcutoff", HTML("<h4><b>Set Cutoff Thresholds</b></h4>"),
choices = list("Max/Min" = 1, "Quantile" = 2, "None" = 3), selected = 2),
conditionalPanel(
condition = "input.HiCcutoff == 1",
textInput3("HiCmax", HTML("<h5><b>Max Value </b></h5>"), value = 100)
),
conditionalPanel(
condition = "input.HiCcutoff == 1",
textInput3("HiCmin", HTML("<h5><b>Min Value </b></h5>"), value = 0)
),
conditionalPanel(
condition = "input.HiCcutoff == 2",
textInput3("quantMax", HTML("<h5><b>Max Quant. </b></h5>"), value = 95)
),
conditionalPanel(
condition = "input.HiCcutoff == 2",
textInput3("quantMin", HTML("<h5><b>Min Quant. </b></h5>"), value = 5)
)),
column(4, selectInput("HiCcolor", HTML("<h4><b>Select Hi-C Color Theme</b></h4>"),
choices = color.choices, selected = 16),
selectInput("missingco", HTML("<h4><b>Specify Missing Data Color</b></h4>"),
choices = missingco.choices, selected = "min"),
checkboxInput("log2hic", "Log Transform Hi-C Values", value = TRUE, width = NULL),
checkboxInput("hiclibnorm", "Normalize for Hi-C Library Complexity", value = FALSE, width = NULL)
)
),
tags$hr(),
actionButton("refresh3", "Refresh Plot"),
style = "default"),
bsCollapsePanel(title = HTML("<h4><b>Advanced Downloading</b></h4>"), value = "bmPanel",
HTML('<h3><b><P ALIGN=Center>Plot Rendering</b></h3>'), tags$br(),
fluidRow(
column(1, tags$br()),
column(5,HTML('<h4><b>Parameters for the <a href="https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev2bitmap.html"
target="_blank">bitmap</a> function</b></h4>'),tags$br(),tags$br(),
textInput3("bm.type",HTML("<h5><b>
Type </b></h5>"), value = "png16m"),
textInput3("bm.res", HTML("<h5><b>Resolution </b></h5>"), value = 72), tags$br(),tags$br(),
downloadButton("bm.down", "Download Custom Plot")
),
column(6,HTML('<h4><b>Plot Dimensions</b></h4>'),
textInput3("bm.height",HTML("<h5><b>Height </b></h5>"), value = 8.5),
textInput3("bm.width", HTML("<h5><b> Width </b></h5>"), value = 11),
textInput3("bm.units", HTML("<h5><b> Units </b></h5>"), value = "in")
)),
tags$hr(),tags$br(),
HTML('<h3><b><P ALIGN=Center>Data Download</b></h3>'),
fluidRow(
column(1, tags$br()),
column(10, HTML("<h5>The left button downloads a .tsv file of all loops that are currently displayed.
The right button downloads a .rds of an R list that summarizes all data being displayed. </b>")),
column(1, tags$br())),tags$br(),
fluidRow(
column(1, tags$br()),
column(5, downloadButton("downloadLoops", "Download Displayed Loops")),
column(5, downloadButton("downloadRDS", "Download All Displayed Data")),
column(1, tags$br())),
tags$hr(),
style = "default")
)),
tabPanel("About",
fluidPage(
headerPanel(
HTML("<h2><b><P ALIGN=Center>Welcome to the DNAlandscapeR Epigenomics Browser</b></h2>
<h3><b><P ALIGN=Center>Aryee Lab</b></h3>")
),
mainPanel(includeHTML("www/welcome.html"),
tags$br(),tags$br(),
width = 12)
)),
tabPanel("Data Descriptions",
fluidPage(
headerPanel(
HTML("<h1><b>Preloaded Data Descriptions</b></h1>")
),
mainPanel(
tags$hr(),
dataTableOutput('preloadedDataDescription'),
tags$hr(),
width = 12
)
)),
tabPanel("Import",
pageWithSidebar(
headerPanel(
tags$h1(tags$b('Add local data'))
),
sidebarPanel(
radioButtons("organismUpload", HTML("<h5><b>Specify organism:</b></h5>"),
choices = list("Human" = 1, "Mouse" = 2),
selected = 1),
tags$hr(),
fileInput("newTrack", h5(tags$b("Add file:")), multiple = FALSE, accept = NULL, width = NULL),
tags$hr(),
textInput3("newTrackName", h5(tags$b("Specify track name:"), value = "")),
tags$hr(),
conditionalPanel(
condition = "input.datType == 6",
textInput3("uploadHiCRes", HTML("<h5><b>Specify Resolutions:</b></h5>"),
value = "1000000,500000,150000,40000,20000")
),
selectInput("datType", label = h5(tags$b("Data type:")),
choices = uploadchoices, #defined in global.R
selected = 1, width = "90%"),
actionButton("addFile", "Add", style='padding:10px; font-size:80%')
),
mainPanel(
HTML("<h4><b>Successfully loaded user files</b></h4>"),
dataTableOutput('dt'),
tags$hr()
)
),
tags$hr(),
pageWithSidebar(
headerPanel(
tags$h1(tags$b('Import AWS Bucket'))
),
sidebarPanel(
textInput("newBucket", h5(tags$b("Specify bucket name:"), value = "")),
tags$hr(),
actionButton("addAWSBucket", "Import", style='padding:10px; font-size:80%')
),
mainPanel(
HTML("<h4><b>Loaded user buckets</b></h4>"),
dataTableOutput('awsLoaded'),
tags$hr()
)
)
),
tabPanel("Guide",
includeMarkdown("www/DNAlandscapeR-help.Rmd")
),
theme = shinytheme("cosmo"),
footer = HTML(paste0('<P ALIGN=Center>DNAlandscapeR. [Version <A HREF="https://github.com/aryeelab/DNAlandscapeR/tree/', sha, '">', short_sha, '</A>] © <A HREF="mailto:[email protected]">Caleb Lareau</A> & Martin Aryee')),
collapsible = TRUE,
fluid = TRUE,
windowTitle = "DNAlandscapeR"
))