Volcano plot part1 #753
Volcano plot part1 #753
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allow selections via plot and/or via datatable filters; added special checkbox selection scenario (checkbox selected genes); cleaned up old part of code that is not used
style.opacity, style.selection_mode and style.special_select_color
allow selections via plot and/or via datatable filters; added special checkbox selection scenario (checkbox selected genes); cleaned up old part of code that is not used
added invisible markers to improve text layout (workaround)
- improved the positioning and margins for the scatterplot - set the font family to the one also used by the data table - moved table searching to views.js - updated the search function to also show a loading icon for the table - fixed a bug which overwrote default settings for the axis instead of deep-copying them
The extra axis labels are different for mRNA expression and protein Switched to the newest version of plotly; removed our drag-functionality and changed to the provided drag-functionality Mini-onco functionality only available in mutations and cna Added a mouse-over icon to the mini-onco and made some layout improvements GeneticProfiles now also returns the datatype Plot subtabs will now only be generated if datatype is not z-score or id doesn't contain z-score Removed Cytoband from the tables to save space
…he positioning of the scatterplot and tables when very few elements were selected (CNA)
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Some suggestions: @aderidder I tried the box selection to select a subset of the dots, but I couldn't figure out a good way to deselect it except refresh the page all together; and I don't find any reset button for that. Maybe a more convenient UI design for this part? @aderidder maybe we can make it more explicit when click on a gene in the table, some bar charts will pop up? I found that feature by accident....otherwise I wouldn't notice. Maybe by default selecting the first gene and show the bar chart from the very beginning? @jjgao Do you think maybe we could just get rid of q-value? And we can get rid of "tendency towards" and just say "co-occurrence"/"mutual exclusive"? Just this page is getting really crowded. |
…ould select a gene. Support for opacity in stacked-histogram
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Hi @yichaoS thanks for the feedback Concerning your first point: yes you're right. Unfortunately I haven't been able to find a good way to do this in the current plotly version. I you'd like more details, let me know and I'll elaborate. I've created an issue for this in the plotly github (plotly/plotly.js#181). Concerning the second issue: I've made some changes and now the mini-onco is visible straight away with the second bar suggesting that the user can select a gene in the table or in the plot. The new version is available on our test server. Thanks, |
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@aderidder very nice work! About Yichao's first point, I think double click on the plot reset the selection, but the table is not updated. It's good idea to remove "tendency towards" in the last column. Let's still keep the q-value there now. |
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Hi @jjgao thanks, glad you like it! |
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@yichaoS do you have any other comments? If not, I'll move it to beta testing. |
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@jjgao I think it looks good. |
| */ | ||
| this.hasLogData = function(){ | ||
| return data_type === "LOG-VALUE"; | ||
| } |
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@jjgao : be aware this could be a pitfall! You need to check if all the relevant genetic profiles on your server have the data type correctly set to LOG-VALUE, otherwise they will not be selected here!
Volcano Plot (ploty) + Mini-onco functionality added to the Enrichtments tab's subtabs
@yichaoS since you're the author of the over representation analysis view and also working with plotly, are you willing to do the code review?