1. GeneTonic
  2. R
  3. GeneTonic-pkg.R
Browse code

fixing namespace after backbone updates

Federico Marini authored on 20/10/2022 09:39:44
Showing1 changed files
R/GeneTonic-pkg.R
History View file @d1a1d48
... ... 
@@ -15,7 +15,7 @@
15 15 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
16 16 
 #'
17 17 
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
18 
-#' @importFrom backbone backbone.extract fdsm fixedrow sdsm universal
18 
+#' @importFrom backbone backbone.extract fdsm fixedrow sdsm
19 19 
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
20 20 
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
21 21 
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
Browse code

fixing typo and re-rendering manpages

Federico Marini authored on 06/04/2022 10:07:44
Showing1 changed files
R/GeneTonic-pkg.R
History View file @bac708b
... ... 
@@ -4,7 +4,7 @@
4 4 
 #' graphical user interface for streamlining the interpretation of RNA-seq data
5 5 
 #'
6 6 
 #' `GeneTonic` simplifies and optimizes the integration of all components of
7 
-#' Diffeential Expression analysis, with functional enrichment analyis and the
7 
+#' Differential Expression analysis, with functional enrichment analysis and the
8 8 
 #' original expression quantifications.
9 9 
 #' It does so in a way that makes it easier to generate insightful observations
10 10 
 #' and hypothesis - combining the benefits of interactivity and reproducibility,
Browse code

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
Showing0 changed files
Browse code

fixing namespace

Federico Marini authored on 27/01/2022 15:25:36
Showing1 changed files
R/GeneTonic-pkg.R
History View file @0982f65
... ... 
@@ -52,17 +52,18 @@
52 52 
 #' @importFrom rmarkdown render
53 53 
 #' @importFrom S4Vectors mcols
54 54 
 #' @importFrom scales alpha muted
55 
-#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
56 
-#' order.dendrogram runif
57 55 
 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
58 56 
 #' @importFrom shinyAce aceEditor
59 57 
 #' @importFrom shinycssloaders withSpinner
60 58 
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
59 
+#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
60 
+#' order.dendrogram runif na.omit
61 61 
 #' @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
65 65 
 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table
66 
+#' head
66 67 
 #' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
67 68 
 #' visOptions
68 69 
 #' @importFrom viridis viridis
Browse code

backbone functions update - hyperg replaced by fixedrow

Federico Marini authored on 19/01/2022 16:22:34
Showing1 changed files
R/GeneTonic-pkg.R
History View file @744c2ee
... ... 
@@ -15,7 +15,7 @@
15 15 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
16 16 
 #'
17 17 
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
18 
-#' @importFrom backbone backbone.extract fdsm hyperg sdsm universal
18 
+#' @importFrom backbone backbone.extract fdsm fixedrow sdsm universal
19 19 
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
20 20 
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
21 21 
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
Browse code

dependencies and imports for geneset upset

Federico Marini authored on 19/01/2022 10:33:29
Showing1 changed files
R/GeneTonic-pkg.R
History View file @20ce1cb
... ... 
@@ -26,6 +26,7 @@
26 26 
 #' @importFrom colorspace rainbow_hcl
27 27 
 #' @importFrom colourpicker colourInput
28 28 
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
29 
+#' @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 "%>%"
Browse code

imports fixed

Federico Marini authored on 14/09/2021 15:53:44
Showing1 changed files
R/GeneTonic-pkg.R
History View file @4a419aa
... ... 
@@ -55,10 +55,12 @@
55 55 
 #' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
56 56 
 #' order.dendrogram runif
57 57 
 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
58 
+#' @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
63 
+#' @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
Browse code

one full round of styler on the codebase, also re-rendering manpages

Federico Marini authored on 27/05/2021 11:22:48
Showing1 changed files
R/GeneTonic-pkg.R
History View file @fc8e87b
... ... 
@@ -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
7 
-#' 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
12 
-#' the live session, and creating an HTML report as an artifact where text,
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
12 
+#' the live session, and creating an HTML report as an artifact where text,
13 13 
 #' code, and output coexist.
14 
-#'
14 
+#'
15 15 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
16 16 
 #'
17 17 
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
... ... 
@@ -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
64 
-#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
64 
+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
65 65 
 #' visOptions
66 66 
 #' @importFrom viridis viridis
67 67 
 #'
Browse code

bye bye bs4TabPanel, it was nice to have you

Federico Marini authored on 26/05/2021 21:14:58
Showing1 changed files
R/GeneTonic-pkg.R
History View file @3af5365
... ... 
@@ -21,7 +21,7 @@
21 21 
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
22 22 
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
23 23 
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
24 
-#' bs4TabPanel bs4TabCard
24 
+#' bs4TabCard
25 25 
 #' @importFrom circlize colorRamp2
26 26 
 #' @importFrom colorspace rainbow_hcl
27 27 
 #' @importFrom colourpicker colourInput
Browse code

filling in manpage for the package

Federico Marini authored on 26/05/2021 09:11:07
Showing1 changed files
R/GeneTonic-pkg.R
History View file @2c89e2a
... ... 
@@ -1,8 +1,17 @@
1 1 
 #' GeneTonic
2 2 
 #'
3 3 
 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
4 
-#'  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
12 
+#' the live session, and creating an HTML report as an artifact where text,
13 
+#' code, and output coexist.
14 
+#'
6 15 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 16 
 #'
8 17 
 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term
Browse code

Added circlize's function to the imports

Federico Marini authored on 13/03/2021 19:45:19
Showing1 changed files
R/GeneTonic-pkg.R
History View file @ba21287
... ... 
@@ -13,6 +13,7 @@
13 13 
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
14 14 
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
15 15 
 #' bs4TabPanel bs4TabCard
16 
+#' @importFrom circlize colorRamp2
16 17 
 #' @importFrom colorspace rainbow_hcl
17 18 
 #' @importFrom colourpicker colourInput
18 19 
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
Browse code

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
Showing0 changed files
Browse code

fixed RMD check for branch

Ludt authored on 18/02/2021 09:49:03
Showing1 changed files
R/GeneTonic-pkg.R
History View file @db1e8aa
... ... 
@@ -13,6 +13,7 @@
13 13 
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
14 14 
 #' bs4TabPanel bs4TabCard
15 15 
 #' @importFrom colorspace rainbow_hcl
16 
+#' @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
Browse code

added imports, reO2 and manpage rendered

Federico Marini authored on 15/02/2021 21:24:24
Showing1 changed files
R/GeneTonic-pkg.R
History View file @9dd9a10
... ... 
@@ -29,8 +29,8 @@
29 29 
 #' @importFrom graphics par plot
30 30 
 #' @importFrom grDevices colorRampPalette rgb col2rgb
31 31 
 #' @importFrom grid gpar
32 
-#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix delete.edges
33 
-#' "%du%" E "E<-" graph.data.frame induced_subgraph
32 
+#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix degree
33 
+#' delete.edges delete_vertices "%du%" E "E<-" graph.data.frame induced_subgraph
34 34 
 #' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
35 35 
 #' @importFrom matrixStats rowSds
36 36 
 #' @importFrom methods is
Browse code

Adding extra imports

Federico Marini authored on 10/02/2021 23:04:10
Showing1 changed files
R/GeneTonic-pkg.R
History View file @dc4a0ac
... ... 
@@ -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
9 
+#' @importFrom backbone backbone.extract fdsm hyperg sdsm universal
9 10 
 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
10 11 
 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
11 12 
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
... ... 
@@ -28,7 +29,8 @@
28 29 
 #' @importFrom graphics par plot
29 30 
 #' @importFrom grDevices colorRampPalette rgb col2rgb
30 31 
 #' @importFrom grid gpar
31 
-#' @importFrom igraph add_edges delete.edges "%du%" E "E<-" graph.data.frame induced_subgraph
32 
+#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix delete.edges
33 
+#' "%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
Browse code

fixing imports and updating namespace

Federico Marini authored on 23/10/2020 23:22:19
Showing1 changed files
R/GeneTonic-pkg.R
History View file @a6ba059
... ... 
@@ -16,7 +16,7 @@
16 16 
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
17 17 
 #' @importFrom dendextend branches_attr_by_clusters set
18 18 
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
19 
-#' @importFrom dplyr arrange desc group_by mutate pull "%>%"
19 
+#' @importFrom dplyr arrange desc group_by mutate pull slice select "%>%"
20 20 
 #' @importFrom DT datatable dataTableOutput renderDataTable formatRound
21 21 
 #' formatStyle JS
22 22 
 #' @importFrom dynamicTreeCut cutreeDynamic
Browse code

color palette now done via colorspace

Federico Marini authored on 01/07/2020 21:01:30
Showing1 changed files
R/GeneTonic-pkg.R
History View file @41c196c
... ... 
@@ -12,6 +12,7 @@
12 12 
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
13 13 
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
14 14 
 #' bs4TabPanel bs4TabCard
15 
+#' @importFrom colorspace rainbow_hcl
15 16 
 #' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
16 17 
 #' @importFrom dendextend branches_attr_by_clusters set
17 18 
 #' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
Browse code

namespace update, import adjusted

Federico Marini authored on 26/06/2020 11:16:16
Showing1 changed files
R/GeneTonic-pkg.R
History View file @748830b
... ... 
@@ -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
49 
-#' @importFrom utils read.delim sessionInfo browseURL citation data
49 
+#' @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
Browse code

fixed imports

Federico Marini authored on 25/06/2020 22:03:09
Showing1 changed files
R/GeneTonic-pkg.R
History View file @9a039f1
... ... 
@@ -19,6 +19,7 @@
19 19 
 #' @importFrom DT datatable dataTableOutput renderDataTable formatRound
20 20 
 #' formatStyle JS
21 21 
 #' @importFrom dynamicTreeCut cutreeDynamic
22 
+#' @importFrom expm "%^%"
22 23 
 #' @importFrom ggforce geom_sina
23 24 
 #' @import ggplot2
24 25 
 #' @importFrom ggrepel geom_label_repel geom_text_repel
... ... 
@@ -26,8 +27,8 @@
26 27 
 #' @importFrom graphics par plot
27 28 
 #' @importFrom grDevices colorRampPalette rgb col2rgb
28 29 
 #' @importFrom grid gpar
29 
-#' @importFrom igraph delete.edges E "E<-" graph.data.frame
30 
-#' permute.vertices V "V<-"
30 
+#' @importFrom igraph add_edges delete.edges "%du%" E "E<-" graph.data.frame induced_subgraph
31 
+#' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist
31 32 
 #' @importFrom matrixStats rowSds
32 33 
 #' @importFrom methods is
33 34 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
Browse code

Enabling export of visNetwork graphs

Federico Marini authored on 03/06/2020 12:47:15
Showing1 changed files
R/GeneTonic-pkg.R
History View file @866b07c
... ... 
@@ -46,7 +46,8 @@
46 46 
 #' @importFrom tidyr separate_rows pivot_longer
47 47 
 #' @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
49 
+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput
50 
+#' visOptions
50 51 
 #' @importFrom viridis viridis
51 52 
 #'
52 53 
 #' @name GeneTonic-pkg
Browse code

Updated namespace with exports and extra import

Federico Marini authored on 17/01/2020 15:38:19
Showing1 changed files
R/GeneTonic-pkg.R
History View file @0b927e8
... ... 
@@ -24,7 +24,7 @@
24 24 
 #' @importFrom ggrepel geom_label_repel geom_text_repel
25 25 
 #' @import GO.db
26 26 
 #' @importFrom graphics par plot
27 
-#' @importFrom grDevices colorRampPalette rgb
27 
+#' @importFrom grDevices colorRampPalette rgb col2rgb
28 28 
 #' @importFrom grid gpar
29 29 
 #' @importFrom igraph delete.edges E "E<-" graph.data.frame
30 30 
 #' permute.vertices V "V<-"
Browse code

Couple of imports fixed

Federico Marini authored on 16/12/2019 20:23:51
Showing1 changed files
R/GeneTonic-pkg.R
History View file @4c6bc53
... ... 
@@ -16,7 +16,8 @@
16 16 
 #' @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 "%>%"
19 
-#' @importFrom DT datatable dataTableOutput renderDataTable
19 
+#' @importFrom DT datatable dataTableOutput renderDataTable formatRound
20 
+#' formatStyle JS
20 21 
 #' @importFrom dynamicTreeCut cutreeDynamic
21 22 
 #' @importFrom ggforce geom_sina
22 23 
 #' @import ggplot2
Browse code

Importing tools as well, and ordered pkg dependencies

Federico Marini authored on 05/12/2019 12:58:43
Showing1 changed files
R/GeneTonic-pkg.R
History View file @8a540d3
... ... 
@@ -43,6 +43,7 @@
43 43 
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
44 44 
 #' @import SummarizedExperiment
45 45 
 #' @importFrom tidyr separate_rows pivot_longer
46 
+#' @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
Browse code

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
Showing1 changed files
R/GeneTonic-pkg.R
History View file @9c3a5f1
... ... 
@@ -43,7 +43,7 @@
43 43 
 #' @importFrom shinyWidgets dropdownButton tooltipOptions
44 44 
 #' @import SummarizedExperiment
45 45 
 #' @importFrom tidyr separate_rows pivot_longer
46 
-#' @importFrom utils read.delim sessionInfo browseURL citation
46 
+#' @importFrom utils read.delim sessionInfo browseURL citation data
47 47 
 #' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
48 48 
 #' @importFrom viridis viridis
49 49 
 #'
Browse code

Adjusting most of the import statements, now in alphabetical order

Federico Marini authored on 21/11/2019 10:22:10
Showing1 changed files
R/GeneTonic-pkg.R
History View file @8918a93
... ... 
@@ -5,44 +5,47 @@
5 5 
 #'
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 7 
 #'
8 
-#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
9 
-#' @importFrom DT dataTableOutput renderDataTable datatable
10 
-#' @importFrom rintrojs introjs introjsUI
11 
-#' @import igraph
12 
-#' @import visNetwork
13 
-#' @importFrom utils read.delim sessionInfo
14 
-#' @importFrom grDevices colorRampPalette rgb
15 
-#' @importFrom RColorBrewer brewer.pal
16 
-#' @importFrom scales alpha muted
17 
-#' @importFrom S4Vectors mcols
18 
-#' @import ggplot2
19 
-#' @importFrom ggrepel geom_label_repel
20 
-#' @import GO.db
21 
-#' @import DESeq2
22 
-#' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
23 
-#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
24 
-#' @importFrom tidyr separate_rows pivot_longer
25 
-#' @importFrom stats var dist hclust
26 
-#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
27 
-#' @importFrom grid gpar
28 
-#' @importFrom matrixStats rowSds
29 
-#' @import SummarizedExperiment
30 
-#' @importFrom methods is
31 
-#' @import pcaExplorer
32 
-#' @import shinycssloaders
8 
+#' @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
39 
-#' @import shinyWidgets
40 
-#' @import ggalluvial
41 
-#' @import viridis
42 
-#' @importFrom dplyr arrange desc group_by mutate
15 
+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
16 
+#' @importFrom dendextend branches_attr_by_clusters set
17 
+#' @importFrom DESeq2 vst counts estimateSizeFactors normalizationFactors sizeFactors
18 
+#' @importFrom dplyr arrange desc group_by mutate pull "%>%"
19 
+#' @importFrom DT datatable dataTableOutput renderDataTable
20 
+#' @importFrom dynamicTreeCut cutreeDynamic
43 21 
 #' @importFrom ggforce geom_sina
22 
+#' @import ggplot2
23 
+#' @importFrom ggrepel geom_label_repel geom_text_repel
24 
+#' @import GO.db
25 
+#' @importFrom graphics par plot
26 
+#' @importFrom grDevices colorRampPalette rgb
27 
+#' @importFrom grid gpar
28 
+#' @importFrom igraph delete.edges E "E<-" graph.data.frame
29 
+#' permute.vertices V "V<-"
30 
+#' @importFrom matrixStats rowSds
31 
+#' @importFrom methods is
32 
+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout add_trace
33 
+#' @importFrom RColorBrewer brewer.pal
34 
+#' @importFrom rintrojs introjs introjsUI
44 35 
 #' @importFrom rlang .data
45 36 
 #' @importFrom rmarkdown render
37 
+#' @importFrom S4Vectors mcols
38 
+#' @importFrom scales alpha muted
39 
+#' @importFrom stats var dist hclust as.dendrogram as.dist cmdscale median
40 
+#' order.dendrogram runif
41 
+#' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
42 
+#' @importFrom shinycssloaders withSpinner
43 
+#' @importFrom shinyWidgets dropdownButton tooltipOptions
44 
+#' @import SummarizedExperiment
45 
+#' @importFrom tidyr separate_rows pivot_longer
46 
+#' @importFrom utils read.delim sessionInfo browseURL citation
47 
+#' @importFrom visNetwork renderVisNetwork visIgraph visNetworkOutput visOptions
48 
+#' @importFrom viridis viridis
46 49 
 #'
47 50 
 #' @name GeneTonic-pkg
48 51 
 #' @docType package
Browse code

Now importing rmarkdown (using render) instead of just suggesting

Federico Marini authored on 15/11/2019 16:36:47
Showing1 changed files
R/GeneTonic-pkg.R
History View file @eb5cf1c
... ... 
@@ -42,6 +42,7 @@
42 42 
 #' @importFrom dplyr arrange desc group_by mutate
43 43 
 #' @importFrom ggforce geom_sina
44 44 
 #' @importFrom rlang .data
45 
+#' @importFrom rmarkdown render
45 46 
 #'
46 47 
 #' @name GeneTonic-pkg
47 48 
 #' @docType package
Browse code

Fixed imports and test for gs_heatmap

Federico Marini authored on 13/11/2019 21:14:09
Showing1 changed files
R/GeneTonic-pkg.R
History View file @2080c6b
... ... 
@@ -23,7 +23,8 @@
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
26 
-#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation
26 
+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation draw
27 
+#' @importFrom grid gpar
27 28 
 #' @importFrom matrixStats rowSds
28 29 
 #' @import SummarizedExperiment
29 30 
 #' @importFrom methods is
Browse code

Documenting and fixing imports after the switch

Federico Marini authored on 13/11/2019 21:07:38
Showing1 changed files
R/GeneTonic-pkg.R
History View file @2ad91d3
... ... 
@@ -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
26 
-#' @import pheatmap
26 
+#' @importFrom ComplexHeatmap Heatmap HeatmapAnnotation
27 27 
 #' @importFrom matrixStats rowSds
28 28 
 #' @import SummarizedExperiment
29 29 
 #' @importFrom methods is
Browse code

using bsCards and showcasing some more of the functionality for the overviews on terms

Federico Marini authored on 31/10/2019 21:23:48
Showing1 changed files
R/GeneTonic-pkg.R
History View file @e1572c3
... ... 
@@ -34,6 +34,7 @@
34 34 
 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
35 35 
 #' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
36 36 
 #' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
37 
+#' bs4TabPanel bs4TabCard
37 38 
 #' @import shinyWidgets
38 39 
 #' @import ggalluvial
39 40 
 #' @import viridis
Browse code

specifying bs4Dash functions to import to avoid namespace collisions

Federico Marini authored on 29/10/2019 16:59:48
Showing1 changed files
R/GeneTonic-pkg.R
History View file @5426785
... ... 
@@ -29,7 +29,11 @@
29 29 
 #' @importFrom methods is
30 30 
 #' @import pcaExplorer
31 31 
 #' @import shinycssloaders
32 
-#' @import bs4Dash
32 
+#' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar
33 
+#' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar
34 
+#' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu
35 
+#' bs4SidebarMenuItem bs4TabItem bs4TabItems bs4ValueBox
36 
+#' bs4ValueBoxOutput renderbs4InfoBox renderbs4ValueBox
33 37 
 #' @import shinyWidgets
34 38 
 #' @import ggalluvial
35 39 
 #' @import viridis
Browse code

rlang import added for avoiding notes

Federico Marini authored on 29/10/2019 15:48:06
Showing1 changed files
R/GeneTonic-pkg.R
History View file @1a512e1
... ... 
@@ -35,6 +35,7 @@
35 35 
 #' @import viridis
36 36 
 #' @importFrom dplyr arrange desc group_by mutate
37 37 
 #' @importFrom ggforce geom_sina
38 
+#' @importFrom rlang .data
38 39 
 #'
39 40 
 #' @name GeneTonic-pkg
40 41 
 #' @docType package
Browse code

added some imports

Federico Marini authored on 29/10/2019 14:51:14
Showing1 changed files
R/GeneTonic-pkg.R
History View file @597f500
... ... 
@@ -20,7 +20,7 @@
20 20 
 #' @import GO.db
21 21 
 #' @import DESeq2
22 22 
 #' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
23 
-#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout
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
26 26 
 #' @import pheatmap
... ... 
@@ -33,6 +33,8 @@
33 33 
 #' @import shinyWidgets
34 34 
 #' @import ggalluvial
35 35 
 #' @import viridis
36 
+#' @importFrom dplyr arrange desc group_by mutate
37 
+#' @importFrom ggforce geom_sina
36 38 
 #'
37 39 
 #' @name GeneTonic-pkg
38 40 
 #' @docType package
Browse code

couple of extra imports

Federico Marini authored on 28/10/2019 13:49:49
Showing1 changed files
R/GeneTonic-pkg.R
History View file @8dd9c73
... ... 
@@ -11,7 +11,7 @@
11 11 
 #' @import igraph
12 12 
 #' @import visNetwork
13 13 
 #' @importFrom utils read.delim sessionInfo
14 
-#' @importFrom grDevices colorRampPalette
14 
+#' @importFrom grDevices colorRampPalette rgb
15 15 
 #' @importFrom RColorBrewer brewer.pal
16 16 
 #' @importFrom scales alpha muted
17 17 
 #' @importFrom S4Vectors mcols
Browse code

imports fixed here and there

Federico Marini authored on 28/10/2019 10:55:30
Showing1 changed files
R/GeneTonic-pkg.R
History View file @432b13d
... ... 
@@ -6,7 +6,6 @@
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 7 
 #'
8 8 
 #' @rawNamespace import(shiny, except = c(renderDataTable, dataTableOutput))
9 
-#' @import shinydashboard
10 9 
 #' @importFrom DT dataTableOutput renderDataTable datatable
11 10 
 #' @importFrom rintrojs introjs introjsUI
12 11 
 #' @import igraph
... ... 
@@ -20,8 +19,8 @@
20 19 
 #' @importFrom ggrepel geom_label_repel
21 20 
 #' @import GO.db
22 21 
 #' @import DESeq2
23 
-#' @importFrom AnnotationDbi Definition
24 
-#' @importFrom plotly ggplotly plotlyOutput renderPlotly
22 
+#' @importFrom AnnotationDbi Definition GOID Term Synonym Secondary
23 
+#' @importFrom plotly ggplotly plotlyOutput renderPlotly plot_ly layout
25 24 
 #' @importFrom tidyr separate_rows pivot_longer
26 25 
 #' @importFrom stats var dist hclust
27 26 
 #' @import pheatmap
... ... 
@@ -32,6 +31,8 @@
32 31 
 #' @import shinycssloaders
33 32 
 #' @import bs4Dash
34 33 
 #' @import shinyWidgets
34 
+#' @import ggalluvial
35 
+#' @import viridis
35 36 
 #'
36 37 
 #' @name GeneTonic-pkg
37 38 
 #' @docType package
Browse code

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
Showing1 changed files
R/GeneTonic-pkg.R
History View file @5334300
... ... 
@@ -30,6 +30,8 @@
30 30 
 #' @importFrom methods is
31 31 
 #' @import pcaExplorer
32 32 
 #' @import shinycssloaders
33 
+#' @import bs4Dash
34 
+#' @import shinyWidgets
33 35 
 #'
34 36 
 #' @name GeneTonic-pkg
35 37 
 #' @docType package
Browse code

inserting cssloaders, with some BioC touch

Federico Marini authored on 17/10/2019 21:00:44
Showing1 changed files
R/GeneTonic-pkg.R
History View file @05cf7a3
... ... 
@@ -29,6 +29,7 @@
29 29 
 #' @import SummarizedExperiment
30 30 
 #' @importFrom methods is
31 31 
 #' @import pcaExplorer
32 
+#' @import shinycssloaders
32 33 
 #'
33 34 
 #' @name GeneTonic-pkg
34 35 
 #' @docType package
Browse code

import fixes for R CMD check

Federico Marini authored on 07/10/2019 08:19:19
Showing1 changed files
R/GeneTonic-pkg.R
History View file @17109d7
... ... 
@@ -27,6 +27,8 @@
27 27 
 #' @import pheatmap
28 28 
 #' @importFrom matrixStats rowSds
29 29 
 #' @import SummarizedExperiment
30 
+#' @importFrom methods is
31 
+#' @import pcaExplorer
30 32 
 #'
31 33 
 #' @name GeneTonic-pkg
32 34 
 #' @docType package
Browse code

Version 0.2.0, with namespace fixes

Federico Marini authored on 07/10/2019 07:26:31
Showing1 changed files
R/GeneTonic-pkg.R
History View file @99e8142
... ... 
@@ -23,7 +23,7 @@
23 23 
 #' @importFrom AnnotationDbi Definition
24 24 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
25 25 
 #' @importFrom tidyr separate_rows pivot_longer
26 
-#' @importFrom stats var
26 
+#' @importFrom stats var dist hclust
27 27 
 #' @import pheatmap
28 28 
 #' @importFrom matrixStats rowSds
29 29 
 #' @import SummarizedExperiment
Browse code

added some specific imports

Federico Marini authored on 06/10/2019 21:10:11
Showing1 changed files
R/GeneTonic-pkg.R
History View file @c85b3d8
... ... 
@@ -11,7 +11,7 @@
11 11 
 #' @importFrom rintrojs introjs introjsUI
12 12 
 #' @import igraph
13 13 
 #' @import visNetwork
14 
-#' @importFrom utils read.delim
14 
+#' @importFrom utils read.delim sessionInfo
15 15 
 #' @importFrom grDevices colorRampPalette
16 16 
 #' @importFrom RColorBrewer brewer.pal
17 17 
 #' @importFrom scales alpha muted
... ... 
@@ -19,10 +19,14 @@
19 19 
 #' @import ggplot2
20 20 
 #' @importFrom ggrepel geom_label_repel
21 21 
 #' @import GO.db
22 
+#' @import DESeq2
22 23 
 #' @importFrom AnnotationDbi Definition
23 24 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
24 25 
 #' @importFrom tidyr separate_rows pivot_longer
26 
+#' @importFrom stats var
25 27 
 #' @import pheatmap
28 
+#' @importFrom matrixStats rowSds
29 
+#' @import SummarizedExperiment
26 30 
 #'
27 31 
 #' @name GeneTonic-pkg
28 32 
 #' @docType package
Browse code

added import for pheatmap

Federico Marini authored on 04/10/2019 10:11:13
Showing1 changed files
R/GeneTonic-pkg.R
History View file @1a6ccf7
... ... 
@@ -22,6 +22,7 @@
22 22 
 #' @importFrom AnnotationDbi Definition
23 23 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
24 24 
 #' @importFrom tidyr separate_rows pivot_longer
25 
+#' @import pheatmap
25 26 
 #'
26 27 
 #' @name GeneTonic-pkg
27 28 
 #' @docType package
Browse code

using pivot function instead of melt, and added roxygen skeletons

Federico Marini authored on 02/10/2019 11:51:30
Showing1 changed files
R/GeneTonic-pkg.R
History View file @ea4947d
... ... 
@@ -21,7 +21,7 @@
21 21 
 #' @import GO.db
22 22 
 #' @importFrom AnnotationDbi Definition
23 23 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
24 
-#' @importFrom tidyr separate_rows
24 
+#' @importFrom tidyr separate_rows pivot_longer
25 25 
 #'
26 26 
 #' @name GeneTonic-pkg
27 27 
 #' @docType package
Browse code

using now geom label repel

Federico Marini authored on 30/09/2019 20:20:30
Showing1 changed files
R/GeneTonic-pkg.R
History View file @a5f0a32
... ... 
@@ -17,6 +17,7 @@
17 17 
 #' @importFrom scales alpha muted
18 18 
 #' @importFrom S4Vectors mcols
19 19 
 #' @import ggplot2
20 
+#' @importFrom ggrepel geom_label_repel
20 21 
 #' @import GO.db
21 22 
 #' @importFrom AnnotationDbi Definition
22 23 
 #' @importFrom plotly ggplotly plotlyOutput renderPlotly
Browse code

added imports

Federico Marini authored on 30/09/2019 20:17:58
Showing1 changed files
R/GeneTonic-pkg.R
History View file @c6cbe2d
... ... 
@@ -14,12 +14,13 @@
14 14 
 #' @importFrom utils read.delim
15 15 
 #' @importFrom grDevices colorRampPalette
16 16 
 #' @importFrom RColorBrewer brewer.pal
17 
-#' @importFrom scales alpha
17 
+#' @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
23 
+#' @importFrom tidyr separate_rows
23 24 
 #'
24 25 
 #' @name GeneTonic-pkg
25 26 
 #' @docType package
Browse code

Adding some more imports

Federico Marini authored on 30/09/2019 09:28:21
Showing1 changed files
R/GeneTonic-pkg.R
History View file @e91300b
... ... 
@@ -15,6 +15,11 @@
15 15 
 #' @importFrom grDevices colorRampPalette
16 16 
 #' @importFrom RColorBrewer brewer.pal
17 17 
 #' @importFrom scales alpha
18 
+#' @importFrom S4Vectors mcols
19 
+#' @import ggplot2
20 
+#' @import GO.db
21 
+#' @importFrom AnnotationDbi Definition
22 
+#' @importFrom plotly ggplotly plotlyOutput renderPlotly
18 23 
 #'
19 24 
 #' @name GeneTonic-pkg
20 25 
 #' @docType package
Browse code

import updates

Federico Marini authored on 27/09/2019 19:12:56
Showing1 changed files
R/GeneTonic-pkg.R
History View file @bb38919
... ... 
@@ -12,6 +12,9 @@
12 12 
 #' @import igraph
13 13 
 #' @import visNetwork
14 14 
 #' @importFrom utils read.delim
15 
+#' @importFrom grDevices colorRampPalette
16 
+#' @importFrom RColorBrewer brewer.pal
17 
+#' @importFrom scales alpha
15 18 
 #'
16 19 
 #' @name GeneTonic-pkg
17 20 
 #' @docType package
Browse code

namespace adjustments to reach 000 in pkg check

Federico Marini authored on 26/09/2019 22:07:24
Showing1 changed files
R/GeneTonic-pkg.R
History View file @87adbb7
... ... 
@@ -5,11 +5,13 @@
5 5 
 #'
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 7 
 #'
8 
+#' @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
14 
+#' @importFrom utils read.delim
13 15 
 #'
14 16 
 #' @name GeneTonic-pkg
15 17 
 #' @docType package
Browse code

Removed Simon from author list

Federico Marini authored on 26/09/2019 21:24:27
Showing1 changed files
R/GeneTonic-pkg.R
History View file @a7a4c25
... ... 
@@ -4,7 +4,6 @@
4 4 
 #'  graphical user interface for...
5 5 
 #'
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 
-#' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
8 7 
 #'
9 8 
 #' @import shinydashboard
10 9 
 #' @importFrom DT dataTableOutput renderDataTable datatable
Browse code

import for roxygen as well

Federico Marini authored on 26/09/2019 21:19:35
Showing1 changed files
R/GeneTonic-pkg.R
History View file @5eab21d
... ... 
@@ -5,6 +5,13 @@
5 5 
 #'
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
7 7 
 #' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
8 
+#'
9 
+#' @import shinydashboard
10 
+#' @importFrom DT dataTableOutput renderDataTable datatable
11 
+#' @importFrom rintrojs introjs introjsUI
12 
+#' @import igraph
13 
+#' @import visNetwork
14 
+#'
8 15 
 #' @name GeneTonic-pkg
9 16 
 #' @docType package
10 17 
 NULL
Browse code

Switched directly to roxygen-markdown docu

Federico Marini authored on 24/06/2019 13:35:21
Showing1 changed files
R/GeneTonic-pkg.R
History View file @1625304
... ... 
@@ -1,6 +1,6 @@
1 1 
 #' GeneTonic
2 2 
 #'
3 
-#' \code{GeneTonic} is a Bioconductor package that provides an interactive Shiny-based
3 
+#' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based
4 4 
 #'  graphical user interface for...
5 5 
 #'
6 6 
 #' @author Federico Marini \email{marinif@@uni-mainz.de}
Browse code

R pkg documentation for the R folder

Federico Marini authored on 24/06/2019 13:33:34
Showing1 changed files
R/GeneTonic-pkg.R
History View file @3df2ac3
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,10 @@
1 
+#' GeneTonic
2 
+#'
3 
+#' \code{GeneTonic} is a Bioconductor package that provides an interactive Shiny-based
4 
+#'  graphical user interface for...
5 
+#'
6 
+#' @author Federico Marini \email{marinif@@uni-mainz.de}
7 
+#' @author Simon Tiado Stahl \email{simon.t.stahl@@gmail.com}
8 
+#' @name GeneTonic-pkg
9 
+#' @docType package
10 
+NULL