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ui-tab-inputdata.R
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ui-tab-inputdata.R
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## ==================================================================================== ##
# START Shiny App for analysis and visualization of transcriptome data.
# Copyright (C) 2016 Jessica Minnier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# You may contact the author of this code, Jessica Minnier, at <minnier@ohsu.edu>
## ==================================================================================== ##
##
## ==================================================================================== ##
## This tab is used to input the count or normalized data files
## ==================================================================================== ##
tabPanel("Input Data",
## ==================================================================================== ##
## Left hand column has the input data settings and options
## ==================================================================================== ##
fluidRow(column(4,wellPanel(
# PDF of instructions link
downloadLink("instructionspdf",label="Download Instructions (pdf)"),
# Upload data from csv, upload data from RData, use example data
radioButtons('data_file_type','Use example file or upload your own data',
c('Upload Data'="upload",
'START RData file'="previousrdata",
'Example Data'="examplecounts"
),selected = "examplecounts"),
# Conditional panels appear based on input.data_file_type selection
conditionalPanel(condition="input.data_file_type=='previousrdata'",
fileInput('rdatafile','Upload START Generated RData File'),
conditionalPanel("output.fileUploaded",
h4(strong("Check data contents then click:")))
),
conditionalPanel(condition="input.data_file_type=='upload'",
radioButtons("inputdat_type","Input Data Type:",
c("Expression data: Gene Counts or log-expression (log2cpms)"="expression_only",
"Analyzed data: Expression Values, p-values, fold changes"="analyzed")),
conditionalPanel(
condition="input.inputdat_type=='expression_only'",
downloadLink("example_counts_file",label="Download Example Count File"),
p(""),
img(src="examplecounts.png",width="100%"),
tags$ul(
tags$li("File must have a header row."),
tags$li("First/Left-hand column(s) must be gene identifiers."),
tags$li("Format expression column names as GROUPNAME_REPLICATE#: Group1_1, Group1_2, Group2_1, Group2_2...")
),
radioButtons("analysis_method","Analysis Method",
c("edgeR"="edgeR",
"voom/limma"="voom",
"Array or counts already normalized, linear models"="linear_model"))
),
conditionalPanel(condition="input.inputdat_type=='analyzed'",
downloadLink("example_analysis_file",label="Download Example Analysis Results File"),
p(""),
img(src="exampleanalysisdata.png",width="100%"),
tags$ul(
tags$li("File must have a header row."),
tags$li("Format expression column names as GROUPNAME_REPLICATE#: Group1_1, Group1_2, Group2_1, Group2_2..."),
tags$li("Number & order of fold changes must MATCH p-value number & order.")
)
),
fileInput('datafile', 'Choose File Containing Data (.CSV)',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
conditionalPanel(condition="input.inputdat_type=='analyzed'",
#checkboxInput('header', 'Header', TRUE),
selectInput("c_geneid1",label="First column # with gene IDs",choices=NULL),
selectInput("c_geneid2",label="Last column # with gene IDs",choices=NULL),
selectInput("c_expr1",label="First column # with expression values",choices=NULL),
selectInput("c_expr2",label="Last column # with expression values",choices=NULL),
selectInput("c_fc1",label="First column # with fold changes",choices=NULL),
selectInput("c_fc2",label="Last column # with fold changes",choices=NULL),
radioButtons("isfclogged",label="Is FC logged? (if false, expression values will be log2-transformed for visualization)",choices=c("Yes (Leave it alone)","No (Log my data please)"),selected="No (Log my data please)"),
selectInput("c_pval1",label="First column # with p-values",choices=NULL),
selectInput("c_pval2",label="Last column # with p-values",choices=NULL),
selectInput("c_qval1",label="First column # with adjusted p-values (can be same columns as p-values)",choices=NULL),
selectInput("c_qval2",label="Last column # with adjusted p-values (can be same columns as p-values)",choices=NULL)
)
),
conditionalPanel("output.fileUploaded",
actionButton("upload_data","Submit Data",
style="color: #fff; background-color: #CD0000; border-color: #9E0000"))
)#,
# add reference group selection
# missing value character?
),#column
## ==================================================================================== ##
## Right hand column shows data input DT and data analysis result DT
## ==================================================================================== ##
column(8,
bsCollapse(id="input_collapse_panel",open="data_panel",multiple = FALSE,
bsCollapsePanel(title="Data Contents: Check Before `Submit`",
value="data_panel",
dataTableOutput('countdataDT')
),
bsCollapsePanel(title="Analysis Results: Ready to View Other Tabs",
value="analysis_panel",
downloadButton('downloadResults_CSV','Save Results as CSV File'),
downloadButton('downloadResults_RData',
'Save Results as START RData File for Future Upload',
class="mybuttonclass"),
dataTableOutput('analysisoutput'),
tags$head(tags$style(".mybuttonclass{background-color:#CD0000;} .mybuttonclass{color: #fff;} .mybuttonclass{border-color: #9E0000;}"))
)
)#bscollapse
)#column
)#fluidrow
)#tabpanel