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New updates #46

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New updates #46

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d7f44da
few improvements to documentation
sk-sahu May 2, 2021
1a59498
about page and few fixes
sk-sahu May 2, 2021
57eb46b
missing import fix
sk-sahu May 2, 2021
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about page and few fixes
  • Loading branch information
@sk-sahu
sk-sahu committed May 2, 2021
commit 1a59498b2890d3a11cffbfa9d664683c676fc7fa
6 changes: 5 additions & 1 deletion R/app_utils.R
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Expand Up @@ -32,4 +32,8 @@ app_noFCmsgPlot <- function(){
"You need to provide foldchange for this."),
cex = 1.6, col = "black")
par(mar = c(5, 4, 4, 2) + 0.1)
}
}

about_md <- function(){
return(paste0(find.package("SigBio"), "/app/about.md"))
}
5 changes: 5 additions & 0 deletions inst/app/about.md
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@@ -0,0 +1,5 @@
**SigBio-Shiny: A standalone interactive application for detecting biological significance on a set of genes**

Homepage: https://github.com/sk-sahu/sig-bio-shiny/

Issue/bug/suggestions: Please create an issue [here](https://github.com/sk-sahu/sig-bio-shiny/issues) or directly ask on [Gitter open chatroom](https://gitter.im/sig-bio-shiny/community)
24 changes: 10 additions & 14 deletions inst/app/app.R
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Expand Up @@ -33,6 +33,8 @@ ENSG00000134690,0.2
ENSG00000065328,1.7
ENSG00000117399,-0.5"

default_gene_type <- "ENSEMBL"

library(shiny)
library(shinydashboard)

Expand All @@ -44,9 +46,8 @@ ui <- dashboardPage(
menuItem("Mapped Ids", tabName = "mapped-ids", icon = icon("dashboard")),
menuItem("Gene Ontology", tabName = "gene-ontology", icon = icon("dashboard")),
menuItem("KEGG", tabName = "kegg", icon = icon("dashboard")),
menuItem("session-info", tabName = "session-info", icon = icon("dashboard")),
menuItem("Help", tabName = "help", icon = icon("dashboard")),
menuItem("About", tabName = "about", icon = icon("dashboard"))
menuItem("Session-info", tabName = "session-info", icon = icon("dashboard")),
menuItem("About", tabName = "about", icon = icon("info-circle"))
)
),
dashboardBody(
Expand All @@ -58,7 +59,7 @@ ui <- dashboardPage(
label = "[Gene] or [Gene,Foldchnage] list:",
height = "150px", width = "230px",
value = example_genelist),
selectInput("id_type", label = "Input gene-id Type:", selected = "ENSEMBL",
selectInput("id_type", label = "Input gene-id Type:", selected = default_gene_type,
choices=c("ENSEMBL", "REFSEQ", "ENTREZID"))
),
box(title = "Organism Input",
Expand Down Expand Up @@ -106,13 +107,8 @@ ui <- dashboardPage(
verbatimTextOutput("sessioninfo")
),

tabItem("help",
includeHTML("")
),

tabItem("about",
icon = icon("info-circle") ,
includeHTML("")
includeMarkdown(SigBio:::about_md())
)
)
)
Expand Down Expand Up @@ -142,7 +138,7 @@ server <- function(input, output) {

incProgress(1/7, detail = paste("Getting Org Database...")) ##### Progress step 1

validated_app_input <- callModule(SigBio:::app_input_validate_server, "input_validate",
validated_app_input <- callModule(SigBio:::app_input_validate_server, "input_validate", session,
input_org = input$org,
input_orgdb = orgdb,
input_ah = ah,
Expand All @@ -169,15 +165,15 @@ server <- function(input, output) {

# all maped ids
if(input$tabs=="mapped-ids"){
callModule(SigBio:::mapids_server, "mapids",
callModule(SigBio:::mapids_server, "mapids", session,
gene_list_uprcase = app_input$gene_list_uprcase,
org_pkg = app_input$org_pkg,
gtf_type = app_input$gtf_type)
}

# gene ontology
if(input$tabs=="gene-ontology"){
callModule(SigBio:::enrichGO_server, "enrichgo",
callModule(SigBio:::enrichGO_server, "enrichgo", session,
gene_list = app_input$gene_list_uprcase,
gene_list_with_fc = app_input$gene_list_with_fc,
entrez_ids_with_fc_vector = app_input$entrez_ids_with_fc_vector,
Expand All @@ -191,7 +187,7 @@ server <- function(input, output) {
if(input$tabs=="kegg"){
incProgress(6/7, detail = paste("Doing KEGG...")) ##### Progress step 6
SigBio:::sigbio_message(paste0("Doing enrichKEGG... "))
callModule(SigBio:::enrichKEGG_server, "enrichkegg",
callModule(SigBio:::enrichKEGG_server, "enrichkegg", session,
gene_list_with_fc = app_input$gene_list_with_fc,
entrez_ids_with_fc_vector = app_input$entrez_ids_with_fc_vector,
entrez_ids_with_fc = app_input$entrez_ids_with_fc,
Expand Down