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ui-tab-analysisres.R
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ui-tab-analysisres.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 <[email protected]>
## ==================================================================================== ##
## ==================================================================================== ##
## Analysis Plots
## ==================================================================================== ##
tabPanel("Analysis Plots",
fluidRow(column(4,wellPanel(
conditionalPanel("input.analysisres_tabset=='Volcano Plot'",
selectizeInput("analysisres_test", label="Select Test for Volcano Plot",
choices=NULL),
numericInput("analysisres_fold_change_cut",
label="Choose log2(Fold Change) Threshold\n(based on your input FCs,
or fitted FCs if your data has been analyzed by START)",min= 0, max=20,value=1),
numericInput("analysisres_pvalcut",
label="Choose P-value Threshold",min=0,max=1,value=0.05),
numericInput("analysisres_fdrcut",
label="Choose adjusted P-value (or FDR) Threshold",min=0,max=1,value=0.05)
),#conditionalpanel
conditionalPanel("input.analysisres_tabset=='Scatterplot of Fold Changes'",
selectizeInput("analysisres_groups",label="Select Groups for Scatterplot",
choices=NULL,
multiple=TRUE,options = list(maxItems = 2)),
radioButtons("scattervaluename",label="Select Scatterplot Value",choices=""),
radioButtons("scattercolor",label="Select Color Factor Value",
choices=c("Sign of FC",
"logFC","p-value","adjusted p-value (q-value)",
"p-value < .1","q-value < .1",
"-log10(p-value)","-log10(q-value)"),
selected = "-log10(p-value)"),
radioButtons("scatterresultsname",label="Select Test for Color Factor",
choices=""),
colourInput("scattercolor_low",label="Select Color - Low Values","blue",
showColour = "background"),
colourInput("scattercolor_hi",label="Select Color - High Values","orange",
showColour = "background")
),#conditionalpanel
selectizeInput("analysisres_genes",label="Select Genes to Highlight",
choices=NULL,
multiple=TRUE)
)#,
#img(src="KCardio_CMYK_4C_pos_small.jpg",height=150,width= 275,align="right")
),#column
column(8,
tabsetPanel(id="analysisres_tabset",
tabPanel(title="Volcano Plot",
#h5(textOutput("corPR")),
#uiOutput("volcanoplot_2groups_ggvisUI"),
#ggvisOutput("volcanoplot_2groups_ggvis")
plotlyOutput("volcanoplot",height=600)
),#tabPanel
tabPanel(title="Scatterplot of Fold Changes",
#h5(textOutput("corPR")),
# uiOutput("scatterplot_fc_2groups_ggvisUI"),
# ggvisOutput("scatterplot_fc_2groups_ggvis")
plotlyOutput("scatterplot",height=600)
)#tabPanel
)#tabsetPanel
)#column
)#fluidrow
) #END tabPanel