pblumenkamp / genexvis Goto Github PK

In GitLab by @[email protected] on Aug 10, 2018, 13:10

Merges deseq2_overview_2 -> development

The original issue

Id: 19
Title: Does not update subset if subset is currently selected

could not be created.
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TODO

In GitLab by @[email protected] on Mar 13, 2018, 12:44

There should be a way to reset/empty the dge object. This includes frontend work and adding new actions and mutations to the vuex store.

In GitLab by @[email protected] on Apr 6, 2018, 14:40

Merges tidy_up_webpack -> development

merging for testing ci-runner

The original issue

Id: 13
Title: Exchange volcano plot series for highcharts zones

could not be created.
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TODO

In GitLab by @[email protected] on Apr 17, 2019, 16:29

DESeq2 Top10 and Overview must get newly formatted since new ESLint update caused many warnings and errors

In GitLab by @jwinter on Aug 31, 2018, 12:32

Merges deseq2_overview_2 -> development

Removed old code, added the column-memory-function at deseq2-overview.

In GitLab by @mmueller on Aug 8, 2019, 10:56

Metadata and DESeq2 data are merged based on full feature IDs. If the IDs do not match fully, import for a gff will be blocked. Might lead to problems, if the user changed IDs during data processing (featureCounts, gff).

The original issue

Id: 17
Title: Histograms for count data

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TODO

In GitLab by @jwinter on Mar 8, 2018, 14:01

Merges patch-1 -> master

In GitLab by @[email protected] on Nov 15, 2018, 14:13

There should be some kind of button to add a gene to the subset.

Button? Link?

In GitLab by @mmueller on Apr 15, 2019, 13:16

• upload of deseq2_results (e.g. _t0_Vs._t1_large.csv) results in gene_0 missing in store

• .csv has 1Mio entries (starting with gene_0)

• DGE store says: 999.999 genes, starting with gene_1

In GitLab by @[email protected] on Mar 28, 2019, 12:46

The "Reset Table" button in DESeq2 Overview does not reset the table completely. After setting a filter in one column and then resetting the table, the filter is still active (only the icon is gone).

In GitLab by @[email protected] on Nov 15, 2018, 14:17

Lowest value should be -3.7

The original issue

Id: 6
Title: Integration of raw data

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TODO

In GitLab by @jwinter on Aug 5, 2018, 11:10

Merges deseq2_overview_2 -> development

DESeq2_overview_2 müsste fertig sein. Zu beachten wäre, dass du an anderer Stelle schon die Farben der Balken geändert hast (DESeq2_Overview, Tabelle, Log2FoldChange).

In GitLab by @[email protected] on Apr 10, 2018, 14:51

Create a range slider with a customizable gradient background as vue component. It can be used to select the intermediate color stop in heat maps. The value of this slider should be mirrored as the center of the gradient.

https://stackoverflow.com/questions/48985608/change-color-gradient-of-input-slider-using-js?rq=1 can be used as a template.

The error message, DESeq2 file does not match the count table, must be improved.

In GitLab by @[email protected] on Jul 17, 2018, 13:33

A lot of warnings appear on the web console if "Deseq2 overview" is opened with the test data.

• ag-grid: invalid gridOptions property 'ob' did you mean any of these:
  groupSuppressBlankHeader,slaveGrids,rowData,columnDefs,excelStyles,pinnedTopRowData,pinnedBottomRowData,components

• gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid gridOptions properties please check: https://www.ag-grid.com/javascript-grid-properties/

• gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

• gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
  GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

• gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

• gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
  GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

• gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

• gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
  GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

• gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

• gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/

In GitLab by @jwinter on Aug 27, 2018, 11:49

Merges top10_genes -> development

In GitLab by @jwinter on Jul 12, 2018, 10:48

Merges deseq2_overview_2 -> development

In GitLab by @jwinter on Jun 20, 2018, 13:23

Merges deseq2_overview_2 -> development

• Extended the parsers "ignore-situations" (2 fields, 1 match AND 1 field, 2 matches)
• Removed "TEST" at Volcano Plot
• Added several "scoped" in "<style>".

Ready to merge.

In GitLab by @[email protected] on Apr 16, 2019, 10:27

For some reason, the download button on each top 10 plot has fewer options than other scatter plots (i.e. volcano plot)

The original issue

Id: 27
Title: Import of multiple count tables

could not be created.
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TODO

In GitLab by @[email protected] on Mar 13, 2018, 12:23

The conditions of a analysis could be guessed with the file name.

• deseq2_results_t0_Vs._t1.csv → condition1: t0; condition2: t1

In GitLab by @[email protected] on Nov 15, 2018, 14:19

Ascending should be descending and vice versa.

Ascending = 1,2,3,4,5
Descending = 5,4,3,2,1

In GitLab by @[email protected] on Mar 21, 2018, 17:27

Merges volcano_plot -> development

First functioning version of volcano plot

In GitLab by @jwinter on Jul 22, 2018, 14:29

Merges deseq2_overview_2 -> development

Folgendes wurde in den letzten Tagen geaddet:

• Farbige Balken für den Log2FoldChange
• Die ersten 2 Balken werden immer angezeigt
• Der Error-Output ist eleminiert.
  Meinen Aufzeichnungen nach ist der Branch "deseq2_overview_2" damit closable.

In GitLab by @[email protected] on Mar 28, 2019, 11:10

Table should use more of vertical space.

In GitLab by @[email protected] on Mar 18, 2020, 11:31

An additional header including the conditions of each column would make the overview table user-friendlier

In GitLab by @[email protected] on Mar 28, 2019, 11:48

Gene names are bigger than their surrounding box in "Current subset" box. The surrounding box should grow with the name length.

In GitLab by @mmueller on Apr 15, 2019, 09:26

• cloned git repository
• ran npm install
• npm run dev resulted in error "TypeError: Cannot read property 'properties' of undefined "
  fixed with changing webpack and webpack-cli to the following in package.json
  (plotly/dash-component-boilerplate#12)

"webpack": "^4.20.2"

"webpack-cli": "^3.1.1"

then ran npm install --save webpack-cli

-> other versions of webpack and webpack-cli not necessary, but the npm install --save webpack-cli seems to be.

In GitLab by @[email protected] on Mar 10, 2018, 17:29

Merges jest_integration -> development

Jest is integrated and tests for dge.js were added

The original issue

Id: 26
Title: counts vs. counts scatter plot

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TODO

In GitLab by @[email protected] on Mar 28, 2019, 12:53

• True/false next to "Current subset:" can be deleted
• A small gap between the genes box and the Clear button
• +/- should be inverted (swap + with - and vice versa)
• bigger margin for the inner box (the one containing all subset genes). The gap between the gene button and the outer box should be increased

In GitLab by @[email protected] on Mar 28, 2018, 13:27

Merges raw_data_integration -> development

add a raw version of feature #6

The original issue

Id: 2
Title: check conditions to be valid in file uploader

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

The original issue

Id: 21
Title: p-Value histogram

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TODO

In GitLab by @rmueller on Jun 12, 2018, 17:28

The original issue

Id: 18
Title: Replace Set by Array for normalizationMethods in Dge

could not be created.
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TODO

In GitLab by @[email protected] on Apr 24, 2018, 20:23

Chart export cannot be recognized as images (see attachment visualizer_heatmap_03)

In GitLab by @[email protected] on Aug 27, 2018, 10:34

Merges deseq2_overview_2 -> development

The original issue

Id: 22
Title: log2 fold change histogram

could not be created.
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TODO

In GitLab by @[email protected] on Mar 28, 2018, 14:53

MA plot for DESeq2 data

In GitLab by @jwinter on Aug 27, 2018, 15:14

Merges deseq2_overview_2 -> development

In GitLab by @[email protected] on Jul 17, 2018, 13:15

Added non-passive event listener to a scroll-blocking 'mousewheel' event. Consider marking event handler as 'passive' to make the page more responsive.

• from 2,000,000 cells upwards the ag-grid table should get replaced by a more efficient (but less features) table (bootstrap table?) (@pblumenk)
• by default, lfcSE, p-value, and stat should be hidden (with an option to show them)
• it should also be possible to hide a comparison completely in the ag-grid table
• there should be an option to download the table (tsv, csv, xlsx) (@pblumenk)
• download the subset (tsv, csv, xlsx) (@pblumenk)

In GitLab by @[email protected] on Mar 28, 2018, 13:35

A visualization of the most significant genes (Top 10?).

• boxplot
• scatter/line plot

In GitLab by @[email protected] on Jul 3, 2018, 13:18

Each tab has a separate store at the moment.

Possible solutions:

• https://github.com/xanf/vuex-shared-mutations
• https://github.com/robinvdvleuten/vuex-persistedstate

In GitLab by @[email protected] on Mar 29, 2018, 17:02

Heat map with gene against sample and the read count visualized with the heat map color