added inst

sigven · Feb 27, 2021 · 9343d78 · 9343d78
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diff --git a/inst/bibliography.bib b/inst/bibliography.bib
@@ -1,4 +1,32 @@
 
+@ARTICLE{Kandasamy2010-te,
+  title    = "{NetPath}: a public resource of curated signal transduction
+              pathways",
+  author   = "Kandasamy, Kumaran and Mohan, S Sujatha and Raju, Rajesh and
+              Keerthikumar, Shivakumar and Kumar, Ghantasala S Sameer and
+              Venugopal, Abhilash K and Telikicherla, Deepthi and Navarro, J
+              Daniel and Mathivanan, Suresh and Pecquet, Christian and
+              Gollapudi, Sashi Kanth and Tattikota, Sudhir Gopal and Mohan,
+              Shyam and Padhukasahasram, Hariprasad and Subbannayya, Yashwanth
+              and Goel, Renu and Jacob, Harrys K C and Zhong, Jun and Sekhar,
+              Raja and Nanjappa, Vishalakshi and Balakrishnan, Lavanya and
+              Subbaiah, Roopashree and Ramachandra, Y L and Rahiman, B Abdul
+              and Prasad, T S Keshava and Lin, Jian-Xin and Houtman, Jon C D
+              and Desiderio, Stephen and Renauld, Jean-Christophe and
+              Constantinescu, Stefan N and Ohara, Osamu and Hirano, Toshio and
+              Kubo, Masato and Singh, Sujay and Khatri, Purvesh and Draghici,
+              Sorin and Bader, Gary D and Sander, Chris and Leonard, Warren J
+              and Pandey, Akhilesh",
+  journal  = "Genome Biol.",
+  volume   =  11,
+  number   =  1,
+  pages    = "R3",
+  month    =  jan,
+  year     =  2010,
+  url      = "http://dx.doi.org/10.1186/gb-2010-11-1-r3",
+  language = "en"
+}
+
 @ARTICLE{Mermel2011-bp,
   title    = "{GISTIC2.0} facilitates sensitive and confident localization of
               the targets of focal somatic copy-number alteration in human

diff --git a/inst/templates/functional_enrichment.Rmd b/inst/templates/functional_enrichment.Rmd
@@ -26,7 +26,7 @@
 show_enrichment_filters <- list()
 missing_enrichment_items <- list()
 eitems <- list()
-for(type in c('go','msigdb','wikipathway','kegg')){
+for(type in c('go','msigdb','wikipathway','kegg','netpath')){
   show_enrichment_filters[[type]] <- F
   missing_enrichment_items[[type]] <- T
   if(NROW(onc_enrich_report[['data']][['enrichment']][[type]]) > 0){
@@ -155,9 +155,14 @@ htmltools::br()
 library(crosstalk)
 
 enrichment_keggdb_display <- onc_enrich_report[['data']][['enrichment']][['kegg']] %>%
-  dplyr::rename(Term = description_link, Enrichment = enrichment_factor, Q_Value = qvalue,  P_Value = pvalue,
-                Gene_Members = gene_symbol_link, DB = db,
-                Exact_Source = exact_source, Background_Ratio = background_ratio, 
+  dplyr::rename(Term = description_link, 
+                Enrichment = enrichment_factor, 
+                Q_Value = qvalue,  
+                P_Value = pvalue,
+                Gene_Members = gene_symbol_link, 
+                DB = db,
+                Exact_Source = exact_source, 
+                Background_Ratio = background_ratio, 
                 Gene_Ratio = gene_ratio, Count = count,
                 P_Value_Cutoff = setting_p_value_cutoff,
                 Q_Value_Cutoff = setting_q_value_cutoff,
@@ -173,10 +178,6 @@ terms_keggdb <- crosstalk::SharedData$new(enrichment_keggdb_display)
 crosstalk::bscols(
   list(
     crosstalk::filter_slider("Enrichment", "Enrichment", terms_keggdb, ~Enrichment)
-  ),
-  list(
-    crosstalk::filter_select("DB", "Signature collection", terms_keggdb, ~DB)
-
   )
 )
 
@@ -228,13 +229,22 @@ enrichment_wikidb_display <- onc_enrich_report[['data']][['enrichment']][['wikip
                 P_Value_Adj_Method, 
                 Min_Geneset_Size, Max_Geneset_Size)
 
+
+terms_wikipathway <- crosstalk::SharedData$new(enrichment_wikidb_display)
+
+crosstalk::bscols(
+  list(
+    crosstalk::filter_slider("Enrichment", "Enrichment", terms_wikipathway, ~Enrichment)
+  )
+)
+
 htmltools::br()
-DT::datatable(enrichment_wikidb_display, escape = F, 
-              extensions=c("Buttons","Responsive"), width = "100%",
+DT::datatable(terms_wikipathway, escape = F, extensions=c("Buttons","Responsive"), width = "100%",
               options=list(buttons = c('csv','excel'),dom = 'Bfrtip')
 )
 
 
+
 ```
 
 
@@ -274,13 +284,21 @@ enrichment_netpath_display <- onc_enrich_report[['data']][['enrichment']][['netp
                 P_Value_Adj_Method, 
                 Min_Geneset_Size, Max_Geneset_Size)
 
+terms_netpath <- crosstalk::SharedData$new(enrichment_netpath_display)
+
+crosstalk::bscols(
+  list(
+    crosstalk::filter_slider("Enrichment", "Enrichment", terms_netpath, ~Enrichment)
+  )
+)
+
 htmltools::br()
-DT::datatable(enrichment_netpath_display, escape = F, 
-              extensions=c("Buttons","Responsive"), width = "100%",
+DT::datatable(terms_netpath, escape = F, extensions=c("Buttons","Responsive"), width = "100%",
               options=list(buttons = c('csv','excel'),dom = 'Bfrtip')
 )
 
 
+
 ```
 
 

diff --git a/inst/templates/onco_enrich_report.Rmd b/inst/templates/onco_enrich_report.Rmd
@@ -3,7 +3,7 @@ title: "OncoEnrichR report - `r onc_enrich_report[['config']][['project_title']]
 date: '`r strftime(Sys.time(), format = "%B %d, %Y")`'
 bibliography: '`r system.file("bibliography.bib",package = "oncoEnrichR")`'
 nocite: |
-  @Kanehisa2000-nm, @Joshi-Tope2005-bw, @Kelder2012-vj, @Ashburner2000-sy, @Von_Mering2005-jy, @Petryszak2016-jp, @Giurgiu2019-yu, @Koscielny2017-ay, @Yu2012-yk, @Clauset2004-ov, @Kleinberg1999-oo, @Hart2016-ic, @Iorio2018-ph, @Subramanian2005-ci, @Uhlen2015-sh, @Uhlen2017-mg, @Jain2019-eh, @Lever2019-xn, @Mermel2011-bp
+  @Kanehisa2000-nm, @Joshi-Tope2005-bw, @Kelder2012-vj, @Ashburner2000-sy, @Von_Mering2005-jy, @Petryszak2016-jp, @Giurgiu2019-yu, @Koscielny2017-ay, @Yu2012-yk, @Clauset2004-ov, @Kleinberg1999-oo, @Hart2016-ic, @Iorio2018-ph, @Subramanian2005-ci, @Uhlen2015-sh, @Uhlen2017-mg, @Jain2019-eh, @Lever2019-xn, @Mermel2011-bp, @Kandasamy2010-te
 output: 
   html_document:
     toc: true
@@ -13,6 +13,8 @@ output:
     toc_depth: 4
     fig_width: 5
     fig_height: 4
+    highlight: null
+    mathjax: null
 ---
 
 

diff --git a/inst/templates/tcga_coexpression.Rmd b/inst/templates/tcga_coexpression.Rmd
@@ -1,8 +1,10 @@
 ### TCGA co-expression {.tabset}
 
-* Using RNA-seq data from ~10,000 tumor samples in TCGA, a co-expression correlation matrix (Pearson rank correlation coefficient) was calculated, indicating pairs of genes that have their expression patterns correlated in tumors
+* Using RNA-seq data from ~9,500 primary tumor samples in TCGA, a co-expression correlation matrix (Pearson rank correlation coefficient) was calculated, indicating pairs of genes that have their expression patterns correlated in tumors
 * Here, we are showing, across the main primary tumor sites in TCGA:
   - Tumor suppressor genes, proto-oncogenes or cancer driver genes with a **strong/very strong** (_r_ >= 0.6 or _r_ <= -0.6 ) correlation to genes in the target set
+  - Here, a maximum of 2500 associations are shown per correlation direction, the
+complete set are listed in the Excel output of oncoEnrichR
 
 
 <br><br>
@@ -20,7 +22,8 @@ for(n in c('Positive','Negative')){
   
     coexp_data[[n]] <- onc_enrich_report[['data']][['tcga']][['co_expression']] %>% 
       dplyr::filter(corrtype == n) %>%
-      dplyr::select(-corrtype)
+      dplyr::select(-corrtype) %>%
+      head(2500)
     
     if(n == 'Negative'){
       coexp_data[[n]] <- coexp_data[[n]] %>%