added filters for filter data. runs but does not filter yet.

server-filterdata.R

@@ -0,0 +1,111 @@
+## ==================================================================================== ##
+# 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 <[email protected]>
+## ==================================================================================== ##
+## 
+
+observe({
+  print("server-datafilter-update-filters")
+  data_analyzed = analyzeDataReactive()
+  tmpdatlong = data_analyzed$data_long
+  tmpynames = tmpdatlong%>%select(-unique_id,-sampleid,-group)%>%colnames()
+  tmpgroups = data_analyzed$group_names
+  tmpsamples = as.character(data_analyzed$sampledata$sampleid)
+  tmpgeneids = data_analyzed$geneids
+  tmpdat = data_analyzed$results
+  tmptests = unique(as.character(tmpdat$test))
+
+  updateSelectizeInput(session,"datafilter_groups", 
+                       choices=tmpgroups,selected=tmpgroups)
+  updateSelectizeInput(session,"datafilter_samples", 
+                       choices=tmpsamples,selected=tmpsamples)
+
+  updateSelectizeInput(session,"datafilter_gene_select",
+                       choices=tmpgeneids)
+
+  updateSelectizeInput(session,"datafilter_selecttest",choices=tmptests)
+
+  updateRadioButtons(session,'datafilter_selectexpr',
+                     choices=sort(tmpynames,decreasing = TRUE))
+
+})
+
+# after selecting test
+
+observe({
+  print("server-datafilter-update-tests")
+
+  if(!(input$datafilter_selecttest=="")) {
+    tmptest = input$datafilter_selecttest
+    # get max abs fold change for this test
+    tmpdat = data_analyzed$results
+    tmpdat = tmpdat%>%filter(test==tmptest)
+    tmpfc = abs(tmpdat$logFC)
+    tmpfc = tmpfc[tmpfc<Inf]
+    tmpmax = max(tmpfc,na.rm=T)
+    if(tmpmax==Inf)
+
+      updateNumericInput(session,"datafilter_fccut",
+                         min=0,max= ceiling(tmpmax),value=0)
+  }
+})
+
+# after selecting expression value
+observe({
+  print("server-datafilter-update-expr")
+  if(!(input$datafilter_selectexpr=="")) {
+    exprname = input$datafilter_selectexpr
+    #calculate miin and max
+    tmpdat = data_analyzed$data_long # add filter by group and sample id
+    tmpmin = min(tmpdat[,colnames(tmpdat)==exprname],na.rm=T)
+    tmpmax = max(tmpdat[,colnames(tmpdat)==exprname],na.rm=T)
+
+    updateNumericInput(session,"datafilter_exprmin",
+                 min=tmpmin,max= tmpmax,value=tmpmin)
+    updateNumericInput(session,"datafilter_exprmax",
+                 min=tmpmin,max= tmpmax,value=tmpmax)
+  }
+})
+
+
+
+#download buttons
+#DF display, make prettier?
+#data summary?
+
+
+
+
+
+
+# if datafilter_fold_change_groups selected
+
+# observe({
+#   group1 = input$datafilter_fold_change_groups[1]
+#   group2 = input$datafilter_fold_change_groups[2]
+#   tmpdatlong%>%filter(group==group1)
+#   tmpdatlong%>%filter(group==group2)
+#   updateNumericInput(session,"datafilter_log2fc_cut",min=0,max=max(abs))
+# })
+
+
+
+
+
+
+

server.R

@@ -28,6 +28,7 @@ shinyServer(function(input, output,session) {
   ## Server functions are divided by tab
   ## 
   source("server-inputdata.R",local = TRUE)
+  source("server-filterdata.R",local = TRUE)
   source("server-dotplot.R",local = TRUE)
   source("server-heatmap.R",local = TRUE)
   source("server-samplegroupplots.R",local=TRUE)

ui-tab-data-output.R

@@ -0,0 +1,96 @@
+## ==================================================================================== ##
+# 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 <[email protected]>
+## ==================================================================================== ##
+## 
+
+## ==================================================================================== ##
+## 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(
+           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(
+
+         )#wellpanel
+         )#column
+         )#fluidRow
+
+         #download results, download START data with current results but filtered gene lists; download count data with filtered gene lists
+)

ui.R

@@ -52,6 +52,7 @@ tagList(
     ## DOWNLOAD DATA TABS
     ## =========================================================================== ##
     source("ui-tab-inputdata.R",local=TRUE)$value,
+    source("ui-tab-data-output.R",local=TRUE)$value,
     ## =========================================================================== ##
     ## Visualization TABS
     ## =========================================================================== ##