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fixing namespace after backbone updates

Federico Marini authored on 20/10/2022 09:39:44
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@@ -15,7 +15,7 @@
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 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
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 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
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-#' @importFrom backbone backbone.extract fdsm fixedrow sdsm universal
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+#' @importFrom backbone backbone.extract fdsm fixedrow sdsm
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 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
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 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
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 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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fixing typo and re-rendering manpages

Federico Marini authored on 06/04/2022 10:07:44
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@@ -4,7 +4,7 @@
4 4
 #' graphical user interface for streamlining the interpretation of RNA-seq data
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 #'
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 #' `GeneTonic` simplifies and optimizes the integration of all components of
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-#' Diffeential Expression analysis, with functional enrichment analyis and the
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+#' Differential Expression analysis, with functional enrichment analysis and the
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 #' original expression quantifications.
9 9
 #' It does so in a way that makes it easier to generate insightful observations
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 #' and hypothesis - combining the benefits of interactivity and reproducibility,
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Merge pull request #32 from federicomarini/gsupset

Gsupset

Federico Marini authored on 30/03/2022 10:05:07 • GitHub committed on 30/03/2022 10:05:07
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fixing namespace

Federico Marini authored on 27/01/2022 15:25:36
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@@ -52,17 +52,18 @@
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 #' @importFrom rmarkdown render
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 #' @importFrom S4Vectors mcols
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 #' @importFrom scales alpha muted
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-#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
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-#' order.dendrogram runif
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 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
58 56
 #' @importFrom shinyAce aceEditor
59 57
 #' @importFrom shinycssloaders withSpinner
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 #' @importFrom shinyWidgets dropdownButton tooltipOptions
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+#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
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+#' order.dendrogram runif na.omit
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 #' @import SummarizedExperiment
62 62
 #' @importFrom tidyr separate_rows pivot_longer
63 63
 #' @importFrom tippy tippy
64 64
 #' @importFrom tools file_ext file_path_sans_ext
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 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table
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+#' head
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 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
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 #' visOptions
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 #' @importFrom viridis viridis
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backbone functions update - hyperg replaced by fixedrow

Federico Marini authored on 19/01/2022 16:22:34
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@@ -15,7 +15,7 @@
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 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
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 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
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-#' @importFrom backbone backbone.extract fdsm hyperg sdsm universal
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+#' @importFrom backbone backbone.extract fdsm fixedrow sdsm universal
19 19
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
20 20
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
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 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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dependencies and imports for geneset upset

Federico Marini authored on 19/01/2022 10:33:29
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@@ -26,6 +26,7 @@
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 #' @importFrom colorspace rainbow_hcl
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 #' @importFrom colourpicker colourInput
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 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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+#' @importFrom ComplexUpset upset intersection_matrix intersection_size
29 30
 #' @importFrom dendextend branches_attr_by_clusters set
30 31
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
31 32
 #' @importFrom dplyr arrange desc group_by mutate pull slice select "%>%"
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imports fixed

Federico Marini authored on 14/09/2021 15:53:44
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@@ -55,10 +55,12 @@
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 #' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
56 56
 #' order.dendrogram runif
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 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
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+#' @importFrom shinyAce aceEditor
58 59
 #' @importFrom shinycssloaders withSpinner
59 60
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
60 61
 #' @import SummarizedExperiment
61 62
 #' @importFrom tidyr separate_rows pivot_longer
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+#' @importFrom tippy tippy
62 64
 #' @importFrom tools file_ext file_path_sans_ext
63 65
 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table
64 66
 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
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one full round of styler on the codebase, also re-rendering manpages

Federico Marini authored on 27/05/2021 11:22:48
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@@ -2,16 +2,16 @@
2 2
 #'
3 3
 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
4 4
 #' graphical user interface for streamlining the interpretation of RNA-seq data
5
-#'  
6
-#' `GeneTonic` simplifies and optimizes the integration of all components of 
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-#' Diffeential Expression analysis, with functional enrichment analyis and the 
5
+#'
6
+#' `GeneTonic` simplifies and optimizes the integration of all components of
7
+#' Diffeential Expression analysis, with functional enrichment analyis and the
8 8
 #' original expression quantifications.
9
-#' It does so in a way that makes it easier to generate insightful observations 
10
-#' and hypothesis - combining the benefits of interactivity and reproducibility, 
11
-#' e.g. by capturing the features and gene sets of interest highlighted during 
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-#' the live session, and creating an HTML report as an artifact where text, 
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+#' It does so in a way that makes it easier to generate insightful observations
10
+#' and hypothesis - combining the benefits of interactivity and reproducibility,
11
+#' e.g. by capturing the features and gene sets of interest highlighted during
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+#' the live session, and creating an HTML report as an artifact where text,
13 13
 #' code, and output coexist.
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-#'  
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+#'
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 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
17 17
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
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@@ -61,7 +61,7 @@
61 61
 #' @importFrom tidyr separate_rows pivot_longer
62 62
 #' @importFrom tools file_ext file_path_sans_ext
63 63
 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table
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-#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput 
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+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
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 #' visOptions
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 #' @importFrom viridis viridis
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 #'
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bye bye bs4TabPanel, it was nice to have you

Federico Marini authored on 26/05/2021 21:14:58
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@@ -21,7 +21,7 @@
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 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
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 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
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-#' bs4TabPanel bs4TabCard
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+#' bs4TabCard
25 25
 #' @importFrom circlize colorRamp2
26 26
 #' @importFrom colorspace rainbow_hcl
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 #' @importFrom colourpicker colourInput
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filling in manpage for the package

Federico Marini authored on 26/05/2021 09:11:07
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@@ -1,8 +1,17 @@
1 1
 #' GeneTonic
2 2
 #'
3 3
 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
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-#'  graphical user interface for...
5
-#'
4
+#' graphical user interface for streamlining the interpretation of RNA-seq data
5
+#'  
6
+#' `GeneTonic` simplifies and optimizes the integration of all components of 
7
+#' Diffeential Expression analysis, with functional enrichment analyis and the 
8
+#' original expression quantifications.
9
+#' It does so in a way that makes it easier to generate insightful observations 
10
+#' and hypothesis - combining the benefits of interactivity and reproducibility, 
11
+#' e.g. by capturing the features and gene sets of interest highlighted during 
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+#' the live session, and creating an HTML report as an artifact where text, 
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+#' code, and output coexist.
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+#'  
6 15
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 16
 #'
8 17
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
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Added circlize's function to the imports

Federico Marini authored on 13/03/2021 19:45:19
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@@ -13,6 +13,7 @@
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 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
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 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
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 #' bs4TabPanel bs4TabCard
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+#' @importFrom circlize colorRamp2
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 #' @importFrom colorspace rainbow_hcl
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 #' @importFrom colourpicker colourInput
18 19
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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Merge pull request #11 from federicomarini/master

Update graphsummary

AnnekathrinSilvia authored on 26/02/2021 10:52:45 • GitHub committed on 26/02/2021 10:52:45
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fixed RMD check for branch

Ludt authored on 18/02/2021 09:49:03
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@@ -13,6 +13,7 @@
13 13
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
14 14
 #' bs4TabPanel bs4TabCard
15 15
 #' @importFrom colorspace rainbow_hcl
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+#' @importFrom colourpicker colourInput
16 17
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
17 18
 #' @importFrom dendextend branches_attr_by_clusters set
18 19
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
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added imports, reO2 and manpage rendered

Federico Marini authored on 15/02/2021 21:24:24
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@@ -29,8 +29,8 @@
29 29
 #' @importFrom graphics par plot
30 30
 #' @importFrom grDevices colorRampPalette rgb col2rgb
31 31
 #' @importFrom grid gpar
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-#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix delete.edges
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-#' "%du%" E "E<-" graph.data.frame induced_subgraph
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+#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix degree
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+#' delete.edges delete_vertices "%du%" E "E<-" graph.data.frame induced_subgraph
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 #' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
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 #' @importFrom matrixStats rowSds
36 36
 #' @importFrom methods is
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Adding extra imports

Federico Marini authored on 10/02/2021 23:04:10
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@@ -6,6 +6,7 @@
6 6
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 7
 #'
8 8
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
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+#' @importFrom backbone backbone.extract fdsm hyperg sdsm universal
9 10
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
10 11
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
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 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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@@ -28,7 +29,8 @@
28 29
 #' @importFrom graphics par plot
29 30
 #' @importFrom grDevices colorRampPalette rgb col2rgb
30 31
 #' @importFrom grid gpar
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-#' @importFrom igraph add_edges delete.edges "%du%" E "E<-" graph.data.frame induced_subgraph
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+#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix delete.edges
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+#' "%du%" E "E<-" graph.data.frame induced_subgraph
32 34
 #' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
33 35
 #' @importFrom matrixStats rowSds
34 36
 #' @importFrom methods is
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fixing imports and updating namespace

Federico Marini authored on 23/10/2020 23:22:19
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@@ -16,7 +16,7 @@
16 16
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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 #' @importFrom dendextend branches_attr_by_clusters set
18 18
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
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-#' @importFrom dplyr arrange desc group_by mutate pull "%>%"
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+#' @importFrom dplyr arrange desc group_by mutate pull slice select "%>%"
20 20
 #' @importFrom DT datatable dataTableOutput renderDataTable formatRound
21 21
 #' formatStyle JS
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 #' @importFrom dynamicTreeCut cutreeDynamic
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color palette now done via colorspace

Federico Marini authored on 01/07/2020 21:01:30
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@@ -12,6 +12,7 @@
12 12
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
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 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
14 14
 #' bs4TabPanel bs4TabCard
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+#' @importFrom colorspace rainbow_hcl
15 16
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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 #' @importFrom dendextend branches_attr_by_clusters set
17 18
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
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namespace update, import adjusted

Federico Marini authored on 26/06/2020 11:16:16
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@@ -46,7 +46,7 @@
46 46
 #' @import SummarizedExperiment
47 47
 #' @importFrom tidyr separate_rows pivot_longer
48 48
 #' @importFrom tools file_ext file_path_sans_ext
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-#' @importFrom utils read.delim sessionInfo browseURL citation data
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+#' @importFrom utils read.delim sessionInfo browseURL citation data write.table
50 50
 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput 
51 51
 #' visOptions
52 52
 #' @importFrom viridis viridis
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fixed imports

Federico Marini authored on 25/06/2020 22:03:09
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@@ -19,6 +19,7 @@
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 #' @importFrom DT datatable dataTableOutput renderDataTable formatRound
20 20
 #' formatStyle JS
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 #' @importFrom dynamicTreeCut cutreeDynamic
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+#' @importFrom expm "%^%"
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 #' @importFrom ggforce geom_sina
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 #' @import ggplot2
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 #' @importFrom ggrepel geom_label_repel geom_text_repel
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@@ -26,8 +27,8 @@
26 27
 #' @importFrom graphics par plot
27 28
 #' @importFrom grDevices colorRampPalette rgb col2rgb
28 29
 #' @importFrom grid gpar
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-#' @importFrom igraph delete.edges E "E<-" graph.data.frame
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-#' permute.vertices V "V<-"
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+#' @importFrom igraph add_edges delete.edges "%du%" E "E<-" graph.data.frame induced_subgraph
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+#' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
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 #' @importFrom matrixStats rowSds
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 #' @importFrom methods is
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 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
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Enabling export of visNetwork graphs

Federico Marini authored on 03/06/2020 12:47:15
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@@ -46,7 +46,8 @@
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 #' @importFrom tidyr separate_rows pivot_longer
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 #' @importFrom tools file_ext file_path_sans_ext
48 48
 #' @importFrom utils read.delim sessionInfo browseURL citation data
49
-#' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
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+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput 
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+#' visOptions
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 #' @importFrom viridis viridis
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 #'
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 #' @name GeneTonic-pkg
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Updated namespace with exports and extra import

Federico Marini authored on 17/01/2020 15:38:19
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@@ -24,7 +24,7 @@
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 #' @importFrom ggrepel geom_label_repel geom_text_repel
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 #' @import GO.db
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 #' @importFrom graphics par plot
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-#' @importFrom grDevices colorRampPalette rgb
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+#' @importFrom grDevices colorRampPalette rgb col2rgb
28 28
 #' @importFrom grid gpar
29 29
 #' @importFrom igraph delete.edges E "E<-" graph.data.frame
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 #' permute.vertices V "V<-"
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Couple of imports fixed

Federico Marini authored on 16/12/2019 20:23:51
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@@ -16,7 +16,8 @@
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 #' @importFrom dendextend branches_attr_by_clusters set
17 17
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
18 18
 #' @importFrom dplyr arrange desc group_by mutate pull "%>%"
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-#' @importFrom DT datatable dataTableOutput renderDataTable
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+#' @importFrom DT datatable dataTableOutput renderDataTable formatRound
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+#' formatStyle JS
20 21
 #' @importFrom dynamicTreeCut cutreeDynamic
21 22
 #' @importFrom ggforce geom_sina
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 #' @import ggplot2
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Importing tools as well, and ordered pkg dependencies

Federico Marini authored on 05/12/2019 12:58:43
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@@ -43,6 +43,7 @@
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 #' @importFrom shinyWidgets dropdownButton tooltipOptions
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 #' @import SummarizedExperiment
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 #' @importFrom tidyr separate_rows pivot_longer
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+#' @importFrom tools file_ext file_path_sans_ext
46 47
 #' @importFrom utils read.delim sessionInfo browseURL citation data
47 48
 #' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
48 49
 #' @importFrom viridis viridis
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Added data docs, edited setup file in test suite. Also added script for generating the RData objects

Federico Marini authored on 29/11/2019 10:09:32
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@@ -43,7 +43,7 @@
43 43
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
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 #' @import SummarizedExperiment
45 45
 #' @importFrom tidyr separate_rows pivot_longer
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-#' @importFrom utils read.delim sessionInfo browseURL citation
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+#' @importFrom utils read.delim sessionInfo browseURL citation data
47 47
 #' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
48 48
 #' @importFrom viridis viridis
49 49
 #'
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Adjusting most of the import statements, now in alphabetical order

Federico Marini authored on 21/11/2019 10:22:10
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@@ -5,44 +5,47 @@
5 5
 #'
6 6
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
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-#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
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-#' @importFrom DT dataTableOutput renderDataTable datatable
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-#' @importFrom rintrojs introjs introjsUI
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-#' @import igraph
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-#' @import visNetwork
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-#' @importFrom utils read.delim sessionInfo
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-#' @importFrom grDevices colorRampPalette rgb
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-#' @importFrom RColorBrewer brewer.pal
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-#' @importFrom scales alpha muted
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-#' @importFrom S4Vectors mcols
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-#' @import ggplot2
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-#' @importFrom ggrepel geom_label_repel
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-#' @import GO.db
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-#' @import DESeq2
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-#' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
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-#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
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-#' @importFrom tidyr separate_rows pivot_longer
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-#' @importFrom stats var dist hclust
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-#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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-#' @importFrom grid gpar
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-#' @importFrom matrixStats rowSds
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-#' @import SummarizedExperiment
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-#' @importFrom methods is
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-#' @import pcaExplorer
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-#' @import shinycssloaders
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+#' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
33 9
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
34 10
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
35 11
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
36 12
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
37 13
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
38 14
 #' bs4TabPanel bs4TabCard
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-#' @import shinyWidgets
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-#' @import ggalluvial
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-#' @import viridis
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-#' @importFrom dplyr arrange desc group_by mutate
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+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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+#' @importFrom dendextend branches_attr_by_clusters set
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+#' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
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+#' @importFrom dplyr arrange desc group_by mutate pull "%>%"
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+#' @importFrom DT datatable dataTableOutput renderDataTable
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+#' @importFrom dynamicTreeCut cutreeDynamic
43 21
 #' @importFrom ggforce geom_sina
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+#' @import ggplot2
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+#' @importFrom ggrepel geom_label_repel geom_text_repel
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+#' @import GO.db
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+#' @importFrom graphics par plot
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+#' @importFrom grDevices colorRampPalette rgb
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+#' @importFrom grid gpar
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+#' @importFrom igraph delete.edges E "E<-" graph.data.frame
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+#' permute.vertices V "V<-"
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+#' @importFrom matrixStats rowSds
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+#' @importFrom methods is
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+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
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+#' @importFrom RColorBrewer brewer.pal
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+#' @importFrom rintrojs introjs introjsUI
44 35
 #' @importFrom rlang .data
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 #' @importFrom rmarkdown render
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+#' @importFrom S4Vectors mcols
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+#' @importFrom scales alpha muted
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+#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
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+#' order.dendrogram runif
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+#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
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+#' @importFrom shinycssloaders withSpinner
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+#' @importFrom shinyWidgets dropdownButton tooltipOptions
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+#' @import SummarizedExperiment
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+#' @importFrom tidyr separate_rows pivot_longer
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+#' @importFrom utils read.delim sessionInfo browseURL citation
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+#' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
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+#' @importFrom viridis viridis
46 49
 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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Now importing rmarkdown (using render) instead of just suggesting

Federico Marini authored on 15/11/2019 16:36:47
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@@ -42,6 +42,7 @@
42 42
 #' @importFrom dplyr arrange desc group_by mutate
43 43
 #' @importFrom ggforce geom_sina
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 #' @importFrom rlang .data
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+#' @importFrom rmarkdown render
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 #'
46 47
 #' @name GeneTonic-pkg
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 #' @docType package
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Fixed imports and test for gs_heatmap

Federico Marini authored on 13/11/2019 21:14:09
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@@ -23,7 +23,8 @@
23 23
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
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 #' @importFrom tidyr separate_rows pivot_longer
25 25
 #' @importFrom stats var dist hclust
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-#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation
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+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
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+#' @importFrom grid gpar
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 #' @importFrom matrixStats rowSds
28 29
 #' @import SummarizedExperiment
29 30
 #' @importFrom methods is
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Documenting and fixing imports after the switch

Federico Marini authored on 13/11/2019 21:07:38
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@@ -23,7 +23,7 @@
23 23
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
24 24
 #' @importFrom tidyr separate_rows pivot_longer
25 25
 #' @importFrom stats var dist hclust
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-#' @import pheatmap
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+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation
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 #' @importFrom matrixStats rowSds
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 #' @import SummarizedExperiment
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 #' @importFrom methods is
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using bsCards and showcasing some more of the functionality for the overviews on terms

Federico Marini authored on 31/10/2019 21:23:48
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@@ -34,6 +34,7 @@
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 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
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 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
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+#' bs4TabPanel bs4TabCard
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 #' @import shinyWidgets
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 #' @import ggalluvial
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 #' @import viridis
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specifying bs4Dash functions to import to avoid namespace collisions

Federico Marini authored on 29/10/2019 16:59:48
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@@ -29,7 +29,11 @@
29 29
 #' @importFrom methods is
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 #' @import pcaExplorer
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 #' @import shinycssloaders
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-#' @import bs4Dash
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+#' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
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+#' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
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+#' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
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+#' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
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+#' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
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 #' @import shinyWidgets
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 #' @import ggalluvial
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 #' @import viridis
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rlang import added for avoiding notes

Federico Marini authored on 29/10/2019 15:48:06
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@@ -35,6 +35,7 @@
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 #' @import viridis
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 #' @importFrom dplyr arrange desc group_by mutate
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 #' @importFrom ggforce geom_sina
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+#' @importFrom rlang .data
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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added some imports

Federico Marini authored on 29/10/2019 14:51:14
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@@ -20,7 +20,7 @@
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 #' @import GO.db
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 #' @import DESeq2
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 #' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
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-#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout
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+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
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 #' @importFrom tidyr separate_rows pivot_longer
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 #' @importFrom stats var dist hclust
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 #' @import pheatmap
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@@ -33,6 +33,8 @@
33 33
 #' @import shinyWidgets
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 #' @import ggalluvial
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 #' @import viridis
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+#' @importFrom dplyr arrange desc group_by mutate
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+#' @importFrom ggforce geom_sina
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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couple of extra imports

Federico Marini authored on 28/10/2019 13:49:49
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@@ -11,7 +11,7 @@
11 11
 #' @import igraph
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 #' @import visNetwork
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 #' @importFrom utils read.delim sessionInfo
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-#' @importFrom grDevices colorRampPalette
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+#' @importFrom grDevices colorRampPalette rgb
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 #' @importFrom RColorBrewer brewer.pal
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 #' @importFrom scales alpha muted
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 #' @importFrom S4Vectors mcols
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imports fixed here and there

Federico Marini authored on 28/10/2019 10:55:30
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@@ -6,7 +6,6 @@
6 6
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
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 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
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-#' @import shinydashboard
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 #' @importFrom DT dataTableOutput renderDataTable datatable
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 #' @importFrom rintrojs introjs introjsUI
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 #' @import igraph
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@@ -20,8 +19,8 @@
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 #' @importFrom ggrepel geom_label_repel
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 #' @import GO.db
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 #' @import DESeq2
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-#' @importFrom AnnotationDbi Definition
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-#' @importFrom plotly ggplotly plotlyOutput renderPlotly
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+#' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
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+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout
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 #' @importFrom tidyr separate_rows pivot_longer
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 #' @importFrom stats var dist hclust
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 #' @import pheatmap
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@@ -32,6 +31,8 @@
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 #' @import shinycssloaders
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 #' @import bs4Dash
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 #' @import shinyWidgets
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+#' @import ggalluvial
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+#' @import viridis
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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added few lines for the required imports - will polish once it is clear which funcs are imported

Federico Marini authored on 27/10/2019 19:38:41
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@@ -30,6 +30,8 @@
30 30
 #' @importFrom methods is
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 #' @import pcaExplorer
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 #' @import shinycssloaders
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+#' @import bs4Dash
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+#' @import shinyWidgets
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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inserting cssloaders, with some BioC touch

Federico Marini authored on 17/10/2019 21:00:44
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@@ -29,6 +29,7 @@
29 29
 #' @import SummarizedExperiment
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 #' @importFrom methods is
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 #' @import pcaExplorer
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+#' @import shinycssloaders
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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import fixes for R CMD check

Federico Marini authored on 07/10/2019 08:19:19
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@@ -27,6 +27,8 @@
27 27
 #' @import pheatmap
28 28
 #' @importFrom matrixStats rowSds
29 29
 #' @import SummarizedExperiment
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+#' @importFrom methods is
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+#' @import pcaExplorer
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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Version 0.2.0, with namespace fixes

Federico Marini authored on 07/10/2019 07:26:31
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@@ -23,7 +23,7 @@
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 #' @importFrom AnnotationDbi Definition
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 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
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 #' @importFrom tidyr separate_rows pivot_longer
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-#' @importFrom stats var
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+#' @importFrom stats var dist hclust
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 #' @import pheatmap
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 #' @importFrom matrixStats rowSds
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 #' @import SummarizedExperiment
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added some specific imports

Federico Marini authored on 06/10/2019 21:10:11
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@@ -11,7 +11,7 @@
11 11
 #' @importFrom rintrojs introjs introjsUI
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 #' @import igraph
13 13
 #' @import visNetwork
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-#' @importFrom utils read.delim
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+#' @importFrom utils read.delim sessionInfo
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 #' @importFrom grDevices colorRampPalette
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 #' @importFrom RColorBrewer brewer.pal
17 17
 #' @importFrom scales alpha muted
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@@ -19,10 +19,14 @@
19 19
 #' @import ggplot2
20 20
 #' @importFrom ggrepel geom_label_repel
21 21
 #' @import GO.db
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+#' @import DESeq2
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 #' @importFrom AnnotationDbi Definition
23 24
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
24 25
 #' @importFrom tidyr separate_rows pivot_longer
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+#' @importFrom stats var
25 27
 #' @import pheatmap
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+#' @importFrom matrixStats rowSds
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+#' @import SummarizedExperiment
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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added import for pheatmap

Federico Marini authored on 04/10/2019 10:11:13
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@@ -22,6 +22,7 @@
22 22
 #' @importFrom AnnotationDbi Definition
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 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
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 #' @importFrom tidyr separate_rows pivot_longer
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+#' @import pheatmap
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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using pivot function instead of melt, and added roxygen skeletons

Federico Marini authored on 02/10/2019 11:51:30
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@@ -21,7 +21,7 @@
21 21
 #' @import GO.db
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 #' @importFrom AnnotationDbi Definition
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 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
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-#' @importFrom tidyr separate_rows
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+#' @importFrom tidyr separate_rows pivot_longer
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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using now geom label repel

Federico Marini authored on 30/09/2019 20:20:30
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@@ -17,6 +17,7 @@
17 17
 #' @importFrom scales alpha muted
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 #' @importFrom S4Vectors mcols
19 19
 #' @import ggplot2
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+#' @importFrom ggrepel geom_label_repel
20 21
 #' @import GO.db
21 22
 #' @importFrom AnnotationDbi Definition
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 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
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added imports

Federico Marini authored on 30/09/2019 20:17:58
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@@ -14,12 +14,13 @@
14 14
 #' @importFrom utils read.delim
15 15
 #' @importFrom grDevices colorRampPalette
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 #' @importFrom RColorBrewer brewer.pal
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-#' @importFrom scales alpha
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+#' @importFrom scales alpha muted
18 18
 #' @importFrom S4Vectors mcols
19 19
 #' @import ggplot2
20 20
 #' @import GO.db
21 21
 #' @importFrom AnnotationDbi Definition
22 22
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
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+#' @importFrom tidyr separate_rows
23 24
 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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Adding some more imports

Federico Marini authored on 30/09/2019 09:28:21
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@@ -15,6 +15,11 @@
15 15
 #' @importFrom grDevices colorRampPalette
16 16
 #' @importFrom RColorBrewer brewer.pal
17 17
 #' @importFrom scales alpha
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+#' @importFrom S4Vectors mcols
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+#' @import ggplot2
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+#' @import GO.db
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+#' @importFrom AnnotationDbi Definition
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+#' @importFrom plotly ggplotly plotlyOutput renderPlotly
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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import updates

Federico Marini authored on 27/09/2019 19:12:56
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@@ -12,6 +12,9 @@
12 12
 #' @import igraph
13 13
 #' @import visNetwork
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 #' @importFrom utils read.delim
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+#' @importFrom grDevices colorRampPalette
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+#' @importFrom RColorBrewer brewer.pal
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+#' @importFrom scales alpha
15 18
 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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namespace adjustments to reach 000 in pkg check

Federico Marini authored on 26/09/2019 22:07:24
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@@ -5,11 +5,13 @@
5 5
 #'
6 6
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #'
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+#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
8 9
 #' @import shinydashboard
9 10
 #' @importFrom DT dataTableOutput renderDataTable datatable
10 11
 #' @importFrom rintrojs introjs introjsUI
11 12
 #' @import igraph
12 13
 #' @import visNetwork
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+#' @importFrom utils read.delim
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 #'
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 #' @name GeneTonic-pkg
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 #' @docType package
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Removed Simon from author list

Federico Marini authored on 26/09/2019 21:24:27
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@@ -4,7 +4,6 @@
4 4
 #'  graphical user interface for...
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 #'
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 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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-#' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
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 #'
9 8
 #' @import shinydashboard
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 #' @importFrom DT dataTableOutput renderDataTable datatable
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import for roxygen as well

Federico Marini authored on 26/09/2019 21:19:35
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@@ -5,6 +5,13 @@
5 5
 #'
6 6
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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 #' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
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+#'
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+#' @import shinydashboard
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+#' @importFrom DT dataTableOutput renderDataTable datatable
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+#' @importFrom rintrojs introjs introjsUI
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+#' @import igraph
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+#' @import visNetwork
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+#'
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 #' @name GeneTonic-pkg
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 #' @docType package
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 NULL
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Switched directly to roxygen-markdown docu

Federico Marini authored on 24/06/2019 13:35:21
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@@ -1,6 +1,6 @@
1 1
 #' GeneTonic
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 #'
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-#' \code{GeneTonic} is a Bioconductor package that provides an interactive Shiny-based
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+#' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
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 #'  graphical user interface for...
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 #'
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 #' @author Federico Marini \email{marinif@@uni-mainz.de}
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R pkg documentation for the R folder

Federico Marini authored on 24/06/2019 13:33:34
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new file mode 100644
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@@ -0,0 +1,10 @@
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+#' GeneTonic
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+#'
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+#' \code{GeneTonic} is a Bioconductor package that provides an interactive Shiny-based
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+#'  graphical user interface for...
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+#'
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+#' @author Federico Marini \email{marinif@@uni-mainz.de}
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+#' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
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+#' @name GeneTonic-pkg
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+#' @docType package
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+NULL