Count number of lines entered in Custom Selection textarea window
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Martin MOKREJŠ
Mar 28, 2023, 5:05:00 PM3/28/23
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Hi everybody,
the **cBioPortal Webinar 4: Group Comparison** https://www.youtube.com/watch?v=Tx4HZCrIe5c is very helpful but I have two suggestions to improve the video and **to improve the web portal software**:
1. At 20:20 you may show the "currently selected" resulted in 136 samples. I would be very helpful to emphasize that by highlighting the **Selected: 136 patients | 136 samples** line in the _Summary_ webpage of the video.
2. Also, in sync with the above, I suggest to improve the web interface so that when a user Copy&Pastes some lines into the textarea window some javascript could count the number of non-empty, ideally-non-redundant, lines with leading and trailing whitespaces stripped off. Would that be already done by your software it would be already shown in the live demo: clicking "currently selected" would result in 136 lines being pasted into the window, similarly, clicking "currently unselected" would enter 50 lines.
3. The "currently selected" is somewhat difficult to understand. In the GUI one can select some checkboxes which lines are then filled with GRAY background. But, later selecting some other checkboxes results in BLUE background. Those previously labelled in gray background cannot be deselected.
My confusion is whether those lines in GRAY in UNION with those in blue are to be entered into the textarea window (not the actually as I found out) or just those selected in BLUE background (corresponding to the 136 or 50 samples in this example).
The software change in point 2 above would be tremendously helpful, helping me to understand what is going on.
I had to replay the video maybe a dozen times to figure out that you selected 136 all KRAS-mutated samples, then did the inverse to select remaining 50 samples, then *cleared* the selection (unclear whether the lines greyed-out or just in *blue* will be cleared, the latter seems true) and then of those 50 samples you selected those 14 which had the assay "Mutation assay" done.
_Note: It does not really mean the KRAS gene was actually covered by any sequencing reads in that region with a coverage above >10x, etc. So it not really sure the gene was not mutated, especially some SV or MNPs could be missed based on coverage and other circumstances._
Byt anyway, your software is fantastic piece of work.
Thank you.
Martin
P.S.: I could not open an an Issue at github at https://github.com/cBioPortal/cbioportal/issues/new , it returns an error 500.
the **cBioPortal Webinar 4: Group Comparison** https://www.youtube.com/watch?v=Tx4HZCrIe5c is very helpful but I have two suggestions to improve the video and **to improve the web portal software**:
1. At 20:20 you may show the "currently selected" resulted in 136 samples. I would be very helpful to emphasize that by highlighting the **Selected: 136 patients | 136 samples** line in the _Summary_ webpage of the video.
2. Also, in sync with the above, I suggest to improve the web interface so that when a user Copy&Pastes some lines into the textarea window some javascript could count the number of non-empty, ideally-non-redundant, lines with leading and trailing whitespaces stripped off. Would that be already done by your software it would be already shown in the live demo: clicking "currently selected" would result in 136 lines being pasted into the window, similarly, clicking "currently unselected" would enter 50 lines.
3. The "currently selected" is somewhat difficult to understand. In the GUI one can select some checkboxes which lines are then filled with GRAY background. But, later selecting some other checkboxes results in BLUE background. Those previously labelled in gray background cannot be deselected.
My confusion is whether those lines in GRAY in UNION with those in blue are to be entered into the textarea window (not the actually as I found out) or just those selected in BLUE background (corresponding to the 136 or 50 samples in this example).
The software change in point 2 above would be tremendously helpful, helping me to understand what is going on.
I had to replay the video maybe a dozen times to figure out that you selected 136 all KRAS-mutated samples, then did the inverse to select remaining 50 samples, then *cleared* the selection (unclear whether the lines greyed-out or just in *blue* will be cleared, the latter seems true) and then of those 50 samples you selected those 14 which had the assay "Mutation assay" done.
_Note: It does not really mean the KRAS gene was actually covered by any sequencing reads in that region with a coverage above >10x, etc. So it not really sure the gene was not mutated, especially some SV or MNPs could be missed based on coverage and other circumstances._
Byt anyway, your software is fantastic piece of work.
Thank you.
Martin
P.S.: I could not open an an Issue at github at https://github.com/cBioPortal/cbioportal/issues/new , it returns an error 500.
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