make shiny open in new tab/window

uzh · Jun 1, 2022 · 51333f6 · 51333f6
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commit 51333f6
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diff --git a/inst/templates/SCFeatBarcoding.Rmd b/inst/templates/SCFeatBarcoding.Rmd
@@ -481,7 +481,7 @@ AUCell_plotTSNE(tSNE=cellsTsne,
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"}
 
 
 ### Data availability

diff --git a/inst/templates/SCLabelClusters.Rmd b/inst/templates/SCLabelClusters.Rmd
@@ -325,7 +325,7 @@ kable_styling("striped", full_width = F, position = "left")
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Celltype Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Celltype Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Celltype Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Celltype Report"),"/sce_h5")}`){target="_blank"}
 
 
 ### Data availability

diff --git a/inst/templates/ScSCE.Rmd b/inst/templates/ScSCE.Rmd
@@ -415,7 +415,7 @@ AUCell_plotTSNE(tSNE=cellsTsne,
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Cluster Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Cluster Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`){target="_blank"}
 
 
 ### Data availability

diff --git a/inst/templates/ScSCECombine.Rmd b/inst/templates/ScSCECombine.Rmd
@@ -300,7 +300,7 @@ p2
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"}
 
 
 ### Methods

diff --git a/inst/templates/ScSeurat.Rmd b/inst/templates/ScSeurat.Rmd
@@ -472,7 +472,7 @@ AUCell_plotTSNE(tSNE=cellsUmap,
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", sample(0:9, size=1), "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {paste0("https://fgcz-shiny.uzh.ch/fgcz_iSEE", sample(0:9, size=1), "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`){target="_blank"}
 
 ### Data availability
 

diff --git a/inst/templates/ScSeuratCombine.Rmd b/inst/templates/ScSeuratCombine.Rmd
@@ -377,7 +377,7 @@ AUCell_plotTSNE(tSNE=cellsTsne,
 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects.
  [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.]
 
-The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`)
+The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"}