Browse code

updated news

Federico Marini authored on 22/04/2023 12:15:12
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2 2
 
3 3
 ## New features
4 4
 
5
-* `enhance_table()` has now the possibility to plot the visual summaries as ridge lines
5
+* `enhance_table()` has now the possibility to plot the visual summaries as ridge lines.
6
+* When plotting the gene expression for the selected features in the gene-geneset-graph box, it is now possible to disable the labels from being displayed (could lead to unnecessary clutter sometimes).
6 7
 
7 8
 ## Other notes
8 9
 
9
-* Fortified the behavior of `gene_plot()` to fail early when providing an invalid value to the `intgroup` parameter
10
+* Fortified the behavior of `gene_plot()` to fail early when providing an invalid value to the `intgroup` parameter.
10 11
 
11 12
 # GeneTonic 2.2.0
12 13
 
Browse code

updated news

Federico Marini authored on 10/03/2023 15:06:48
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4 4
 
5 5
 * `enhance_table()` has now the possibility to plot the visual summaries as ridge lines
6 6
 
7
+## Other notes
8
+
9
+* Fortified the behavior of `gene_plot()` to fail early when providing an invalid value to the `intgroup` parameter
10
+
7 11
 # GeneTonic 2.2.0
8 12
 
9 13
 ## New features
Browse code

updated news

Federico Marini authored on 10/03/2023 14:27:17
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1
+# GeneTonic 2.4.0
2
+
3
+## New features
4
+
5
+* `enhance_table()` has now the possibility to plot the visual summaries as ridge lines
6
+
1 7
 # GeneTonic 2.2.0
2 8
 
3 9
 ## New features
Browse code

updating news

Federico Marini authored on 07/10/2022 13:26:11
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3 3
 ## New features
4 4
 
5 5
 * `gs_heatmap` gains the `winsorize_threshold` parameter, to control the behavior of the geneset heatmap in presence of extreme values, either negative or positive ones. If not specified, the heatmap is not introducing any winsorization.
6
+* `map2color()` has a behavior that better accounts for asymmetric ranges of values. This propagates to some of the functions that use it for mapping to colors, such as `enrichment_map()`, or `ggs_backbone()`.
6 7
 
7 8
 ## Other notes
8 9
 
9 10
 * Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 
10 11
 * Fixed the label namings for the `gs_heatmap` function
11 12
 * The `enhance_table()` function can handle the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost). It also presents an informative message on which genesets/genes are potentially responsible for the behavior. 
12
-
13
+* Some additional checks are in place for controlling the cases where the `z_score` of a geneset is detected as NA (e.g. because there was a mismatch between gene names and identifiers in the annotation).
14
+ 
13 15
 # GeneTonic 2.0.0
14 16
 
15 17
 ## New features
Browse code

Merge branch 'master' into heatmap_winsorized

# Conflicts:
# DESCRIPTION

Federico Marini authored on 06/10/2022 16:13:21
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Browse code

updated NEWS

Federico Marini authored on 05/10/2022 19:01:06
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4 4
 
5 5
 * Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 
6 6
 * Fixed the label namings for the `gs_heatmap` function
7
+* The `enhance_table()` function can handle the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost). It also presents an informative message on which genesets/genes are potentially responsible for the behavior. 
7 8
 
8 9
 # GeneTonic 2.0.0
9 10
 
Browse code

updated news

Federico Marini authored on 21/09/2022 15:29:43
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1 1
 # GeneTonic 2.2.0
2 2
 
3
+## New features
4
+
5
+* `gs_heatmap` gains the `winsorize_threshold` parameter, to control the behavior of the geneset heatmap in presence of extreme values, either negative or positive ones. If not specified, the heatmap is not introducing any winsorization.
6
+
3 7
 ## Other notes
4 8
 
5 9
 * Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 
Browse code

updated news

Federico Marini authored on 03/08/2022 08:37:44
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3 3
 ## Other notes
4 4
 
5 5
 * Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 
6
+* Fixed the label namings for the `gs_heatmap` function
6 7
 
7 8
 # GeneTonic 2.0.0
8 9
 
Browse code

updated NEWS

Federico Marini authored on 10/06/2022 14:22:06
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1
+# GeneTonic 2.2.0
2
+
3
+## Other notes
4
+
5
+* Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 
6
+
1 7
 # GeneTonic 2.0.0
2 8
 
3 9
 ## New features
Browse code

updated news

Federico Marini authored on 06/04/2022 10:07:19
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50 50
 
51 51
 * `gs_heatmap()` has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
52 52
 * `gs_heatmap()` handles the colors in a consistent way over the different executions, without relying on the random palettes provided by the `Heatmap`'s annotation functionality - could have been misleading if encountering too similar hues are randomly picked
53
-* the plots obtained via `gs_mds()` and `gs_volcano()` now always display the line segments for the data points to be labeled (increasing the readability - as "matching back the label to the drawed circle" - thanks for the suggestion!)
53
+* the plots obtained via `gs_mds()` and `gs_volcano()` now always display the line segments for the data points to be labeled (increasing the readability - as "matching back the label to the drawn circle" - thanks for the suggestion!)
54 54
 
55 55
 # GeneTonic 1.2.0
56 56
 
Browse code

updated NEWS.md

Federico Marini authored on 30/03/2022 10:15:50
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6 6
 * The `GeneSpector` functionality in the Welcome panel provides a means to explore any gene in the expression set, coloring and grouping by any experimental covariate of interest
7 7
 * It is possible to enter a set of genes and genesets in the Bookmarks panel, and these can be doubled checked against the available features of the current `GeneTonicList` - this, combined to the upload functionality, makes it possible to easily compare different `gtl` objects
8 8
 * The `GeneTonic` app has a button to export the currently provided dataset - regardless of the input format - as a `GeneTonicList`. This is especially useful if one is providing the individual components (`dds`, `res_de`, `res_enrich`, `annotation_obj`) and would like to obtain the correct serialized object 
9
+* `gs_upset` adds the possibility to represent the results of enrichment analyses as upset plots, with the option to decorate them with DE-related information
9 10
 
10 11
 ## Other notes
11 12
 
Browse code

updated news

Federico Marini authored on 29/03/2022 10:55:58
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4 4
 
5 5
 * `GeneTonic` now offers the possibility to upload a `GeneTonicList` at runtime. This makes it possible to use the app as a server-like dashboard, which runs by default on no dataset provided, and populates its components upon successfully providing the data as expected
6 6
 * The `GeneSpector` functionality in the Welcome panel provides a means to explore any gene in the expression set, coloring and grouping by any experimental covariate of interest
7
+* It is possible to enter a set of genes and genesets in the Bookmarks panel, and these can be doubled checked against the available features of the current `GeneTonicList` - this, combined to the upload functionality, makes it possible to easily compare different `gtl` objects
8
+* The `GeneTonic` app has a button to export the currently provided dataset - regardless of the input format - as a `GeneTonicList`. This is especially useful if one is providing the individual components (`dds`, `res_de`, `res_enrich`, `annotation_obj`) and would like to obtain the correct serialized object 
7 9
 
8 10
 ## Other notes
9 11
 
Browse code

Updated news

Federico Marini authored on 28/03/2022 15:42:41
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1
-# GeneTonic 1.8.0
1
+# GeneTonic 2.0.0
2 2
 
3 3
 ## New features
4 4
 
5
-* 
5
+* `GeneTonic` now offers the possibility to upload a `GeneTonicList` at runtime. This makes it possible to use the app as a server-like dashboard, which runs by default on no dataset provided, and populates its components upon successfully providing the data as expected
6
+* The `GeneSpector` functionality in the Welcome panel provides a means to explore any gene in the expression set, coloring and grouping by any experimental covariate of interest
6 7
 
7 8
 ## Other notes
8 9
 
Browse code

updating the news for 1.7.2

Federico Marini authored on 19/01/2022 10:50:54
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1
+# GeneTonic 1.8.0
2
+
3
+## New features
4
+
5
+* 
6
+
7
+## Other notes
8
+
9
+* The manuscript about `GeneTonic` is now published on BMC Bioinformatics at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5 - the citation item has been updated accordingly
10
+* The jittered position in the `gene_plot` is now completely reproducible, by setting a seed internally in the jitter generating function
11
+
1 12
 # GeneTonic 1.6.0
2 13
 
3 14
 ## New features
Browse code

updated news for version 1.5.5

Federico Marini authored on 17/09/2021 12:52:09
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3 3
 ## New features
4 4
 
5 5
 * `GeneTonic` can now accept the input of `clusterProfiler`'s gene set enrichment analysis functions (`gseGO` and `GSEA`), as implemented in the `shake_gsenrichResult()` function
6
+* Below each plot and interactive widget, we provide a button that opens up a modal window where the code required to reproduce that output is shown as a snippet. These can be readily copied in extended reports or used to document the exploratory process.
6 7
 
7 8
 ## Other notes
8 9
 
Browse code

updated news

Federico Marini authored on 13/07/2021 22:08:26
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1 1
 # GeneTonic 1.6.0
2 2
 
3
+## New features
4
+
5
+* `GeneTonic` can now accept the input of `clusterProfiler`'s gene set enrichment analysis functions (`gseGO` and `GSEA`), as implemented in the `shake_gsenrichResult()` function
6
+
3 7
 ## Other notes
4 8
 
5 9
 * The manuscript about `GeneTonic` is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1 - the citation item has been updated accordingly
Browse code

updated news, and bumped up the version requirement for bs4Dash

Federico Marini authored on 27/05/2021 07:35:03
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1
-# GeneTonic 1.4.0
1
+# GeneTonic 1.6.0
2 2
 
3 3
 ## Other notes
4 4
 
5 5
 * The manuscript about `GeneTonic` is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1 - the citation item has been updated accordingly
6
+* `GeneTonic`'s Shiny app now uses the latest version of `bs4Dash`, which introduced some breaking changes. Most elements should be now available as they were in the original implementation
6 7
 
7 8
 # GeneTonic 1.4.0
8 9
 
Browse code

updated news

Federico Marini authored on 25/05/2021 10:15:25
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1 1
 # GeneTonic 1.4.0
2 2
 
3
+## Other notes
4
+
5
+* The manuscript about `GeneTonic` is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1 - the citation item has been updated accordingly
6
+
7
+# GeneTonic 1.4.0
8
+
3 9
 ## New features
4 10
 
5 11
 * The main function `GeneTonic()` gains an extra parameter, `gtl` - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single serialized object), while the functionality stays unaltered. 
Browse code

updated news

Federico Marini authored on 05/05/2021 15:25:03
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17 17
 
18 18
 * A new function, `summarize_ggs_hubgenes()`, builds a DT `datatable` for the Gene-Geneset panel. This table lists the individual genes of the input data and their respective degree in the Gene-Geneset graph. Furthermore, `action buttons` linking to the NCBI, GeneCards and GTEx databases are included for each gene.
19 19
 
20
+* `gene_plot()` gains the extra `labels_display` argument to control whether the labels are at all shown; now the display of the labels is also respecting the jitter of the points
21
+
20 22
 ## Other notes
21 23
 
22 24
 * `gs_heatmap()` has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
Browse code

updated news

Federico Marini authored on 03/05/2021 15:58:40
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@@ -21,6 +21,7 @@
21 21
 
22 22
 * `gs_heatmap()` has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
23 23
 * `gs_heatmap()` handles the colors in a consistent way over the different executions, without relying on the random palettes provided by the `Heatmap`'s annotation functionality - could have been misleading if encountering too similar hues are randomly picked
24
+* the plots obtained via `gs_mds()` and `gs_volcano()` now always display the line segments for the data points to be labeled (increasing the readability - as "matching back the label to the drawed circle" - thanks for the suggestion!)
24 25
 
25 26
 # GeneTonic 1.2.0
26 27
 
Browse code

Updated NEWS

Federico Marini authored on 13/03/2021 19:48:53
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@@ -20,6 +20,7 @@
20 20
 ## Other notes
21 21
 
22 22
 * `gs_heatmap()` has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
23
+* `gs_heatmap()` handles the colors in a consistent way over the different executions, without relying on the random palettes provided by the `Heatmap`'s annotation functionality - could have been misleading if encountering too similar hues are randomly picked
23 24
 
24 25
 # GeneTonic 1.2.0
25 26
 
Browse code

Version bump, 1.3.5

Federico Marini authored on 10/03/2021 12:46:01
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15 15
 
16 16
 * `gs_summary_overview()` can also generate bar plots instead of the default segment-dot (lollipop) plots.
17 17
 
18
-* A new function, `summarize_ggs_hubgenes()`, builds a DT `datatable` for the Gene-Geneset panel. This table lists the individual genes of the input data and their respective degree in the Gene-Geneset graph. Furthermore, `action buttons` linking to the NCBI, Genecards and GTEx databases are included for each gene.
18
+* A new function, `summarize_ggs_hubgenes()`, builds a DT `datatable` for the Gene-Geneset panel. This table lists the individual genes of the input data and their respective degree in the Gene-Geneset graph. Furthermore, `action buttons` linking to the NCBI, GeneCards and GTEx databases are included for each gene.
19 19
 
20 20
 ## Other notes
21 21
 
Browse code

Added summary_ggs_hubgenes to News and tour

Ludt authored on 10/03/2021 10:02:37
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10 10
 
11 11
 * The `ggs_backbone()` function can extract the bipartite graph backbone from the Gene-Geneset graph, this can be further explored below the main element in the Gene-Geneset panel. Once the backbone is created, you are one step away from checking out the genes that act as "hubs" in the Gene-Geneset graph, and possibly identify the nodes playing an essential role based on their connectivity.
12 12
 
13
-* A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
13
+* A new function, `signature_volcano()`, adds a signature volcano plot to the Gene-Geneset panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
14 14
   The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.
15 15
 
16
-* `gs_summary_overview()` can also generate bar plots instead of the default segment-dot (lollipop) plots
16
+* `gs_summary_overview()` can also generate bar plots instead of the default segment-dot (lollipop) plots.
17
+
18
+* A new function, `summarize_ggs_hubgenes()`, builds a DT `datatable` for the Gene-Geneset panel. This table lists the individual genes of the input data and their respective degree in the Gene-Geneset graph. Furthermore, `action buttons` linking to the NCBI, Genecards and GTEx databases are included for each gene.
17 19
 
18 20
 ## Other notes
19 21
 
Browse code

Added news on ggs_backbone()

Federico Marini authored on 09/03/2021 14:26:54
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8 8
   
9 9
 * A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
10 10
 
11
+* The `ggs_backbone()` function can extract the bipartite graph backbone from the Gene-Geneset graph, this can be further explored below the main element in the Gene-Geneset panel. Once the backbone is created, you are one step away from checking out the genes that act as "hubs" in the Gene-Geneset graph, and possibly identify the nodes playing an essential role based on their connectivity.
12
+
11 13
 * A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
12 14
   The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.
13 15
 
Browse code

Version 1.3.4, updated news

Federico Marini authored on 03/03/2021 21:05:40
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11 11
 * A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
12 12
   The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.
13 13
 
14
-* `gs_summary_overview` can also generate bar plots instead of the default segment-dot (lollipop) plots
14
+* `gs_summary_overview()` can also generate bar plots instead of the default segment-dot (lollipop) plots
15
+
16
+## Other notes
17
+
18
+* `gs_heatmap()` has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
15 19
 
16 20
 # GeneTonic 1.2.0
17 21
 
Browse code

Version bump, 1.3.3 + updated NEWS on the GeneTonic_list()

Federico Marini authored on 26/02/2021 22:32:56
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@@ -4,6 +4,7 @@
4 4
 
5 5
 * The main function `GeneTonic()` gains an extra parameter, `gtl` - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single serialized object), while the functionality stays unaltered. 
6 6
   The same `gtl` parameter is also exposed in other functions of the package - see the vignette for some examples, or check the documentation of each specific function.
7
+  To create this object in a standardized manner, the function `GeneTonic_list()` is now available.
7 8
   
8 9
 * A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
9 10
 
Browse code

Apply suggestions from code review

Federico Marini authored on 25/02/2021 18:15:58 • GitHub committed on 25/02/2021 18:15:58
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7 7
   
8 8
 * A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
9 9
 
10
-* A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot display the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
10
+* A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
11 11
   The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.
12 12
 
13 13
 * `gs_summary_overview` can also generate bar plots instead of the default segment-dot (lollipop) plots
Browse code

Merge branch 'master' into volcano_plot

Federico Marini authored on 24/02/2021 21:38:48 • GitHub committed on 24/02/2021 21:38:48
Showing 0 changed files
Browse code

Changed files according to pull request volcano plot #9

Ludt authored on 24/02/2021 17:53:09
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@@ -2,11 +2,14 @@
2 2
 
3 3
 ## New features
4 4
 
5
-* The main function `GeneTonic()` gains an extra parameter, `gtl` - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single seralized object), while the functionality stays unaltered. 
5
+* The main function `GeneTonic()` gains an extra parameter, `gtl` - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single serialized object), while the functionality stays unaltered. 
6 6
   The same `gtl` parameter is also exposed in other functions of the package - see the vignette for some examples, or check the documentation of each specific function.
7 7
   
8 8
 * A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
9 9
 
10
+* A new function, `signature_volcano()`, adds a signature volcano plot to the `Gene-Geneset` panel. This plot display the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. 
11
+  The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.
12
+
10 13
 # GeneTonic 1.2.0
11 14
 
12 15
 ## New features
Browse code

Updated news

Federico Marini authored on 19/02/2021 20:42:34
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@@ -7,6 +7,8 @@
7 7
   
8 8
 * A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
9 9
 
10
+* `gs_summary_overview` can also generate bar plots instead of the default segment-dot (lollipop) plots
11
+
10 12
 # GeneTonic 1.2.0
11 13
 
12 14
 ## New features
Browse code

Version bump, 1.3.1, updated NEWS

Federico Marini authored on 06/02/2021 20:29:39
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@@ -1,3 +1,12 @@
1
+# GeneTonic 1.4.0
2
+
3
+## New features
4
+
5
+* The main function `GeneTonic()` gains an extra parameter, `gtl` - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single seralized object), while the functionality stays unaltered. 
6
+  The same `gtl` parameter is also exposed in other functions of the package - see the vignette for some examples, or check the documentation of each specific function.
7
+  
8
+* A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see `gs_fuzzyclustering()`. It returns a table with additional information on the cluster of genesets and the status of each set in the group.  
9
+
1 10
 # GeneTonic 1.2.0
2 11
 
3 12
 ## New features
Browse code

Updated news

Federico Marini authored on 02/07/2020 21:07:41
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1 1
 # GeneTonic 1.2.0
2 2
 
3
+## New features
4
+
5
+* The geneset distillery is officially open! `GeneTonic` offers functionality to aggregate together gene sets into overarching biological themes, based on a network-based refinement of the enrichment map. 
6
+  Corresponding graphical functionalities are also extended to accommodate meta-genesets.
7
+  An efficient implementation for the Markov clustering on graph objects is also provided
8
+  
9
+* `GeneTonic` can now receive the input of many other tools for functional enrichment analysis - this includes the output (text export) of DAVID (`shake_davidResult`), enrichr (from website and via the package, with `shake_enrichrResult`), fgsea (`shake_fgseaResult`), and g:Profiler (with `shake_gprofilerResult`, which can handle the textual output from the website, as well the one from the call to the `gost` in `gprofiler2`)
10
+
11
+* An export button to a `SummarizedExperiment` object for `iSEE` and its underlying machinery has been added. If the visualization options in `GeneTonic` are not exactly what you would expect, you might find an excellent venue in the `iSEE` framework
12
+
3 13
 ## Other notes
4 14
 
5 15
 * Added an additional mechanism for safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the `GO.db` package, or also mistyped if entered by hand at some point.
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+* `gs_heatmap` has a new parameter, `plot_title`, to override the title to be displayed and set it to any custom string
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+* It is now possible to save a snapshot of the graphs created with `visNetwork`
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+* The Gene Box now also contains links to the GTEx portal for the selected feature
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+* `export_to_sif` enables to export a graph object to a text file, encoded with the SIF format
6 20
 
7 21
 # GeneTonic 1.0.0
8 22
 
Browse code

Updated news

Federico Marini authored on 04/05/2020 15:03:12
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+# GeneTonic 1.2.0
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+
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+## Other notes
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+
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+* Added an additional mechanism for safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the `GO.db` package, or also mistyped if entered by hand at some point.
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+
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+# GeneTonic 1.0.0
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+
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+## Other notes
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+
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+* `GeneTonic` has become a part of Bioconductor!
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+
1 13
 # GeneTonic 0.99.0
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3 15
 ## Other notes
Browse code

All fit for Bioc Submission - version 0.99.0

Federico Marini authored on 04/02/2020 13:32:24
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+# GeneTonic 0.99.0
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+
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+## Other notes
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+
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+* `GeneTonic` is now submitted to Bioconductor!
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+
1 7
 # GeneTonic 0.10.0
2 8
 
3 9
 ## New features
Browse code

Version 0.10.0, updated news - soon to be up for Bioc submission

Federico Marini authored on 04/02/2020 13:17:24
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+# GeneTonic 0.10.0
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+
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+## New features
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+
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+* The functions for comparing different `res_enrich`, namely `gs_radar`, `gs_summary_overview_pair`, and `gs_horizon` were internally rewritten to accept correctly the comparison elements
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+* The vignette now covers completely the usage cases, with the full description of the user interface of `GeneTonic`
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+* The introductory tours are available for all the main panels of `GeneTonic`. Feel free to try them out!
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+
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+## Other notes
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+
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+* Some widgets have been added in the UI of `GeneTonic` to enable finer control of the output aspect
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+* Examples and unit tests have been further expanded, with better messages for checking progress
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+* `check_colors` verify that color palettes are correctly provided
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+* Info on `GeneTonic` is now provided with modal dialog windows, rather than in a separate tab
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+* The tab names in the main app were slightly edited to better describe their content
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+* The info boxes are now shown with a uniform style, based on the `bs4Card` UI element
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+* The UI elements have now a better spacing throughout the different tabs
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+* Soon the package will be submitted to Bioconductor!
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+
1 20
 # GeneTonic 0.9.0
2 21
 
3 22
 ## New features
Browse code

Version 0.9.1 - bump + update dates

Federico Marini authored on 23/01/2020 19:21:37
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 * Added link to the demo instance
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 * Added examples for overlap functions, gene info buttons, map2color, and deseqresult2df
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 * Extended documentation of some parameters
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-* Some functions have gained an alias for calling them: `gs_spider` is equivalent to `gs_radar`, and `gs_sankey` is equivalent to `gs_alliuvial`
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+* Some functions have gained an alias for calling them: `gs_spider` is equivalent to `gs_radar`, and `gs_sankey` is equivalent to `gs_alluvial`
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21 21
 # GeneTonic 0.8.0
22 22
 
Browse code

Updated news for upcoming 0.9.0

Federico Marini authored on 10/01/2020 11:51:15
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+# GeneTonic 0.9.0
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+
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+## New features
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+
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+* `GeneTonic` sports a blazing new hex sticker - say bye to the original draft!
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+* The overview DT `datatable`s has some styling with color bars - e.g. for DE results - to enhance the visual perception of numeric values (e.g. log2FoldChange)
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+* `gs_heatmap` can now take a custom list of gene identifiers (when no geneset is passed)
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+* The color palettes in enrichment maps now respect the values and the range specified of the numeric values to be used for mapping to colors
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+* `gs_mds` is now optionally returning a data.frame, to be further used for custom plotting or downstream processing
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+* `gs_summary_overview` now has coloring enabled by the variable of choice
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+
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+## Other notes
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+
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+* The UI has received some restyling (e.g. in the choice of the icons for the dropdown menus, or the name of some buttons)
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+* Added tour contents for most of the functionality
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+* Added link to the demo instance
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+* Added examples for overlap functions, gene info buttons, map2color, and deseqresult2df
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+* Extended documentation of some parameters
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+* Some functions have gained an alias for calling them: `gs_spider` is equivalent to `gs_radar`, and `gs_sankey` is equivalent to `gs_alliuvial`
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+
1 21
 # GeneTonic 0.8.0
2 22
 
3 23
 ## New features
Browse code

Version 0.8.0 - bumped, and added NEWS

Federico Marini authored on 04/12/2019 17:04:33
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+# GeneTonic 0.8.0
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+
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+## New features
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+
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+* `GeneTonic` now delivers bundled example objects to make examples and tests slim
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+* `gs_volcano` can now plot points by different colors according to the columns of interest
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+* `GeneTonic` has a fully fledged manual describing its functionality and user interface
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+
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+## Other notes
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+
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+* Now using ids for genes and genesets for exchanging information in the app
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+* Added examples for all functions
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+* Most tabs have working tours - anchor and text elements
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+
1 15
 # GeneTonic 0.7.0
2 16
 
3 17
 ## New features
Browse code

Version 0.7.0, also with updated NEWS.md

Federico Marini authored on 21/11/2019 22:18:45
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+# GeneTonic 0.7.0
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+
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+## New features
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+
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+* Introduced a uniform interface for calculating different similarity/distance matrices. This enables the usage in the different functions that might need such matrices for further downstream processing (e.g. `enrichment_map()`, `gs_mds()`)
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+* First appearance of `gs_dendro()` to display distance matrices with some visualization sugar, as an alternative to other methods
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+* The `n_gs` and `gs_ids` are exposed to more functions to enable custom subsets of the enrichment results to be inspected
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+
1 9
 # GeneTonic 0.6.0
2 10
 
3 11
 ## New features
Browse code

Bump to version 0.6.0 - also updated NEWS

Federico Marini authored on 13/11/2019 22:03:44
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+# GeneTonic 0.6.0
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+
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+## New features
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+
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+* `gs_heatmap` now relies on `ComplexHeatmap`, to avoid the issues with Shiny of not displaying the outputs in the app, and enabling a comfortable heatmap annotation
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+* Many functions gain the possibility to pass a set of custom geneset identifiers to be added to the top N sets (default): among these, `gs_mds`, `gs_volcano` (parameter: `gs_labels`), `gs_alluvial`, `ggs_network`, `enrichment_map`, and `enhance_table` (using `gs_ids`)
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+
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+## Other notes
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+
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+* `gs_ggheatmap` got renamed to `gs_scoresheat`
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+* The report generated from the bookmarked content is expanded in its default content
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+
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 # GeneTonic 0.5.0
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3 15
 ## New features
Browse code

Bump to v0.5.0, with start of reporting and shaker_ functions

Federico Marini authored on 08/11/2019 14:11:13
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+# GeneTonic 0.5.0
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+
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+## New features
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+
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+* `GeneTonic` now enforces a format for `res_enrich`, and provides some conversion functions, `shake_*()`. Requirements are specified in the documentation, if an appropriate converter does not (yet) exist.
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+* The reporting feature is active to some extent on the bookmarked content.
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+
1 8
 # GeneTonic 0.4.0
2 9
 
3 10
 ## New features
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5
-* added functionality for bookmarking
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-* bookmarking can work (PoP) by pressing a key (left control)!
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+* Added functionality for bookmarking
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+* Bookmarking can work (PoP) by pressing a key (left control)!
7 14
 * `gene_plot` can enforce a plot type overriding the default based on the number of samples per condition
8 15
 * `GeneTonic` uses now `bs4Dash` and many of its nice features, replacing the previous implementation based on `shinydashboard`
9 16
 
Browse code

added NEWS and bumped to 0.4.0

Federico Marini authored on 30/10/2019 12:53:30
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+# GeneTonic 0.4.0
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+
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+## New features
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+
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+* added functionality for bookmarking
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+* bookmarking can work (PoP) by pressing a key (left control)!
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+* `gene_plot` can enforce a plot type overriding the default based on the number of samples per condition
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+* `GeneTonic` uses now `bs4Dash` and many of its nice features, replacing the previous implementation based on `shinydashboard`
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+
1 10
 # GeneTonic 0.3.0
2 11
 
3 12
 ## Other notes
Browse code

done reordering the arguments in uniform way

Federico Marini authored on 24/10/2019 12:19:32
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+# GeneTonic 0.3.0
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+
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+## Other notes
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+
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+* Rearranging the order of parameters to harmonize it across functions, and uniforming similarly called parameters
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+
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 # GeneTonic 0.2.0
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3 9
 ## New features
Browse code

Version 0.2.0, with namespace fixes

Federico Marini authored on 07/10/2019 07:26:31
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+# GeneTonic 0.2.0
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+
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+## New features
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+
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+* added geneset scoring calculation and corresponding heatmap
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+
1 7
 # GeneTonic 0.1.0
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3 9
 ## New features
Browse code

Version bump to 0.1.0, yay

Federico Marini authored on 04/10/2019 20:42:53
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+# GeneTonic 0.1.0
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+
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+## New features
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+
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+* much of the functionality available, in a proof of concept format
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+
1 7
 # GeneTonic 0.0.1
2 8
 
3 9
 ## New features
Browse code

Added file for documenting the NEWS in markdown format

Federico Marini authored on 24/06/2019 23:03:01
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new file mode 100644
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+# GeneTonic 0.0.1
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+
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+## New features
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+
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+* backbone of the project started!