/
ui-tab-filterdata.R
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ui-tab-filterdata.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 filter the data, can be saved in various formats after filtering
## ==================================================================================== ##
tabPanel("Filter Data",
## ==================================================================================== ##
## Left hand column has the filtera settings and options
## ==================================================================================== ##
fluidRow(column(4,wellPanel(
h5("Note: this does not redo any analysis, it merely filters the data already analyzed based on gene identifiers or sample/group names."),
selectizeInput("datafilter_groups", label="Select Groups",
choices=NULL,
multiple=TRUE),
selectizeInput("datafilter_samples", label="Select Samples",
choices=NULL,
multiple=TRUE),
checkboxInput("datafilter_genelist","Filter by gene names",value=FALSE), #upload a file of gene names
conditionalPanel("input.datafilter_genelist==true",
selectizeInput("datafilter_gene_select","Search gene names.",choices=NULL,multiple=TRUE),
fileInput('datafilter_gene_file', 'Or, upload file containing gene IDs\n(one row per gene)',
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv'))
),
# this is complicated since need to calculate fold change based on expression, but we may not know if that
# expression value is logged or not, so how do we get fold change vs log fold change from an unknown value? needs more work
# checkboxInput("datafilter_fc","Filter by fold change for a pair of groups",
# value=FALSE),
# conditionalPanel(condition="input.datafilter_fc==true",
# selectizeInput("datafilter_fold_change_groups", label="Select 2 Groups (numerator first, denominator second)",
# choices=NULL,
# selected=NULL,
# multiple=TRUE,options = list(maxItems = 2)),
# numericInput("datafilter_log2fc_cut",
# label="Choose abs(Log2FC) Minimum",
# min= 0, max=Inf,value=0),
# radioButtons("datafilter_log2fc_direction",label = "Restrict Direction of FC",
# choices=c("No","Up in first group","Down in first group"))
# ),#conditionalpanel
checkboxInput("datafilter_signif","Filter by significance",
value=FALSE),
conditionalPanel(condition="input.datafilter_signif==true",
selectizeInput("datafilter_selecttest","Select Test",choices=NULL),
numericInput("datafilter_fccut",label="Minimum absolute value of Log2 Fold Change",
min=0,max= 20,value=1),
radioButtons("datafilter_logfc_dir",label="Direction of Fold Change",
choices=c("Both"="both","Up in first group"="up","Down in first group"="down")),
numericInput("datafilter_qvaluecut",label="Maximim Q-value (FDR)",
min=0,max= 1,value=1),
numericInput("datafilter_pvaluecut",label="Maximim P-value",
min=0,max= 1,value=1)
),
checkboxInput("datafilter_expr","Filter by expression",
value=FALSE),
conditionalPanel(condition="input.datafilter_expr==true",
radioButtons("datafilter_selectexpr",label="Select Expression Value",choices=""),
numericInput("datafilter_exprmin",label="Filter by minimum expression (remove genes with minimum expression lower than this value)",
min=0,max= 1000,value=1),
numericInput("datafilter_exprmax",label="Filter by maximum expression (remove genes with maximum expression lower than this value)",
min=0,max= 1000,value=1)
)
)#wellpanel
),#column
## ==================================================================================== ##
## Right hand column shows data input DT and data analysis result DT
## ==================================================================================== ##
column(8,wellPanel(
h4(textOutput("nrow_filterdata")),
downloadButton('download_filtered_data_csv','Save Filtered Results as CSV File'),
dataTableOutput('filterdataoutput')
)#wellpanel
)#column
)#fluidRow
#download results, download START data with current results but filtered gene lists; download count data with filtered gene lists
)