adding version 1

README.md

@@ -2,36 +2,36 @@ Author: Min Kim <MinS.Kim@UTSouthwestern.edu> and Spencer Barnes <Spencer.Barnes
 Date: April 20, 2017    
 Description: Shiny app for analyzing TCGA data for frequently asked requests through the Help-Desk.    
 
-Project name     Cancer type
-ACC		 Adrenocortical Carcinoma 
-BLCA             Bladder Urothelial Carcinoma 
-BRCA             Breast Invasive Carcinoma
-CESC             Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
-CHOL             Cholangiocarcinoma
-COAD		 Colon Adenocarcinoma
-DLBC		 Lymphoid Neoplasm Diffuse Large B-cell Lymphoma	
-GBM		 Glioblastoma Multiforme
-HNSC		 Head and Neck Squamous Cell Carcinoma
-KICH 		 Kidney Chromophobe
-KIRC	   	 Kidney Renal Clear Cell Carcinoma
-KIRP 		 Kidney Renal Papillary Cell Carcinoma
-LAML		 Acute Myeloid Leukemia
-LGG  		 Brain Lower Grade Glioma
-LIHC	         Liver Hepatocellular Carcinoma
-LUAD  		 Lung Adenocarcinoma
-LUSC             Lung Squamous Cell Carcinoma
-MESO		 Mesothelioma
-OV		 Ovarian Serous Cystadenocarcinoma
-PAAD		 Pancreatic Adenocarcinoma
-PCPG		 Pheochromocytoma and Paraganglioma
-PRAD   		 Prostate Adenocarcinoma
-READ		 Rectum Adenocarcinoma
-SARC		 Sarcoma
-SKCM		 Skin Cutaneous Melanoma
-TGCT	 	 Testicular Germ Cell Tumors
-THCA 		 Thyroid Carcinoma
-THYM	 	 Thymoma
-UCEC		 Uterine Corpus Endometrial Carcinoma
-UCS	 	 Uterine Carcinosarcoma
-UVM	 	 Uveal Melanoma
+Project name     Cancer type   
+ACC		 Adrenocortical Carcinoma   
+BLCA             Bladder Urothelial Carcinoma   
+BRCA             Breast Invasive Carcinoma   
+CESC             Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma   
+CHOL             Cholangiocarcinoma   
+COAD		 Colon Adenocarcinoma   
+DLBC		 Lymphoid Neoplasm Diffuse Large B-cell Lymphoma   
+GBM		 Glioblastoma Multiforme   
+HNSC		 Head and Neck Squamous Cell Carcinoma   
+KICH 		 Kidney Chromophobe   
+KIRC	   	 Kidney Renal Clear Cell Carcinoma   
+KIRP 		 Kidney Renal Papillary Cell Carcinoma   
+LAML		 Acute Myeloid Leukemia   
+LGG  		 Brain Lower Grade Glioma   
+LIHC	         Liver Hepatocellular Carcinoma   
+LUAD  		 Lung Adenocarcinoma   
+LUSC             Lung Squamous Cell Carcinoma   
+MESO		 Mesothelioma   
+OV		 Ovarian Serous Cystadenocarcinoma   
+PAAD		 Pancreatic Adenocarcinoma   
+PCPG		 Pheochromocytoma and Paraganglioma   
+PRAD   		 Prostate Adenocarcinoma   
+READ		 Rectum Adenocarcinoma   
+SARC		 Sarcoma   
+SKCM		 Skin Cutaneous Melanoma   
+TGCT	 	 Testicular Germ Cell Tumors   
+THCA 		 Thyroid Carcinoma   
+THYM	 	 Thymoma   
+UCEC		 Uterine Corpus Endometrial Carcinoma   
+UCS	 	 Uterine Carcinosarcoma   
+UVM	 	 Uveal Melanoma   
 

scripts/ui.R

 shinyUI(
-  pageWithSidebar(
-    headerPanel("TGCA Analysis"),
-    sidebarPanel(
-      selectInput("operation","Select Plot Type",choices = c("Pancan","Survival")),
-      conditionalPanel(condition = "input.operation=='Pancan'",
-                       selectInput("cancerType","Select one or more cancer types",
-                                   choices = substr(list.files("../Expression/",pattern=".txt"),1,
-                                                    nchar(list.files("../Expression/",pattern=".txt"))-4),
-                                   multiple = TRUE),
-                       textInput("gene","Please input one gene of interest",placeholder = "Gene name ie 'TRIM21'")
-                       ),
-      conditionalPanel(condition="input.operation=='Survival'",
-                       selectInput("cancerType2","Select a cancer type",
-                                   choices = substr(list.files("../Expression/",pattern=".txt"),1,
-                                                    nchar(list.files("../Expression/",pattern=".txt"))-4)),
-                       textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie 'TRIM21'",value="TRIM21"),
-                       sliderInput("cut.off","Select a cutoff value",min = .10,max=.50,step = .05,value = .25)
+  fluidPage(
+    headerPanel("TCGA Analysis"),
+    sidebarLayout(
+      sidebarPanel(
+        selectInput("operation","Select Plot Type",choices = c("Boxplot","Survival")),
+        conditionalPanel(condition = "input.operation=='Boxplot'",
+                         selectInput("cancerType","Select one or more cancer types",
+                                     choices = substr(list.files("../Expression/",pattern=".txt"),1,
+                                                      nchar(list.files("../Expression/",pattern=".txt"))-4),
+                                     multiple = TRUE),
+                         textInput("gene","Please input one gene of interest",placeholder = "Gene name ie TRIM21")
+        ),
+        conditionalPanel(condition="input.operation=='Survival'",
+                         selectInput("cancerType2","Select a cancer type",
+                                     choices = substr(list.files("../Expression/",pattern=".txt"),1,
+                                                      nchar(list.files("../Expression/",pattern=".txt"))-4)),
+                         textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie BRCA1"),
+                         selectInput("operation2","Select automatic or manual cutoff", choices = c("Automatic", "Manual"))
+                         
+        ),
+        conditionalPanel(condition="input.operation2=='Manual' & input.operation=='Survival'",
+                         sliderInput("cut.off","Select a cutoff value",min = .10,max=.50,step = .05,value = .25)
+        ),
+        actionButton("go","GO")
+        
       ),
-      actionButton("go","GO")
-      #conditionalPanel(condition = "input.operation=='Pancan'"
-                       
-      #                 )
-      #selectInput("Distribution", "Select dist type", 
-      #            choices=c("normal","expo")),
-      #sliderInput("sampleSize","Select sample size: ", 
-      #            min=100,max=5000,value=1000,step=100),
-      #conditionalPanel(condition = "input.Distribution=='normal'",
-      #                 textInput("Mean","Plase Select the mean",10),
-      #                 textInput("sd","Please Select Standard Deviation",3)),
-      #conditionalPanel(condition="input.Distribution == 'expo'",
-      #                 textInput("lambda","Pleas select Expo Lambda",1)
-      #)
-    ),
-    mainPanel(
-      plotOutput("myPlot")
+      mainPanel(
+        plotOutput("myPlot"),
+        downloadButton('downloadplot',"Download Figure")
+      )
+      
     )
-    
   )
 )