cmap / morpheus.js Goto Github PK

https://software.broadinstitute.org/morpheus/

I simply get:
Error
Oops, something went wrong. Please try again.

IE version 11.

Sometimes right-click dialog for column metadata is displayed incorrectly (see the screenshot). It happens after I do hierarchical clustering.

Hi,

It looks like there is a possible bug here:

https://github.com/cmap/morpheus.js/blob/master/index.html#L67

I believe that in line 67 (https://github.com/cmap/morpheus.js/blob/master/index.html#L67) the code should use function then, not done. So the code should be:

morpheus.Util.getText(params.url).then(function (text) {

What do you think?

EDIT:

Similarly:

Line 70 should use catch, instead of fail
Line 73 should use finally, instead of always

When I export a heatmap to svg or png, I get the entire heatmap information including row annotations. However, when I export to PDF the row annotations are missing. The row annotation header, eg Gene is visible, but not the actual annotation (gene symbol).

The exported PDF is set to "fit to window".

Hi!

Thanks for the presentation of Morpheus today :).

The link in the README seems to be broken (https://joshua-gould.github.io/morpheus.js/). Is it instead https://clue.io/morpheus/?

Thanks!

I cannot seem to filter columns on multiple categories.

Here is an example from a public data set.

Steps to recreate:

1. I loaded up the AML Mutation Data Set.
2. Clicked Tools --> Filter
3. Clicked Columns
4. Clicked "Pass all filters"
5. Clicked Add
6. Selected Gender --> Female

At this point, the matrix filters nicely.

7. Clicked Add
8. Selected Ethnicity --> Not Hispanic or Latino

At this point, the matrix is filtered by ethnicity, but my original gender filter no longer works. If I click male/female, still nothing happens. Clicking pass all filters also seems to have no effect.

Say I want to sort columns by two categories.
Usual way to do that in a grid is to sort by one, then sort by the second one.
If the sort is stable, this will result in columns sorted by the second category, but within cols with the same second category, they should remain sorted by the first category.

Seem that it's not the case for morpheus, which limits ad-hoc analysis that can be performed.

Steps to reproduce:

• taken https://software.broadinstitute.org/morpheus/
• select "Preloaded Datasets"
• select "Acute Myeloid Leukemia (LAML)"
• "GENE Expression" -> "Open"
• in the zoom menu "Fit Columns To Window"
• click "mRNAseq_cluster" column category to sort by.
• now click "gender" to sort by.

Expected: two groups by gender (it is) and within each of them sorted by "mRNAseq_cluster" (same order if mRNAseq_cluster in both gender groups).
Observed: mRNAseq_cluster order is scrambled.

Is it possible to load morpheus session files from a URL location? That would be useful for sharing preconfigured views of data.

• Loading a dataset works, for example:
  https://software.broadinstitute.org/morpheus/?json={%22dataset%22%3A%22%2F%2Fs3.amazonaws.com%2Frn-test-data%2Ftest.gct%22}%0A

• But it fails if I provide it a Json formatted session file
  https://software.broadinstitute.org/morpheus/?json={%22dataset%22%3A%22%2F%2Fs3.amazonaws.com%2Frn-test-data%2Ftest.json%22}%0A

However downloading the same session file and manually opening it also works.

If some wells have an empty string for an annotation, they show up in filtering as an invisible row with an invisible (but still clickable) checkbox. Below is an example of this checkbox being checked for a group of "" moas.

When filtering a dataset based on row/column titles, the window does not adjust to length of the name correctly. The name seems to become two lines and becomes unreadable (example below):

Hi,
I am using Morpheus to visualize a gene expression heatmap. The heatmap cell grid are not removed even though I unchecked the 'show grid' under Option->Display.
Is there a way to remove cell box grid completely?

Hi Josh,

There are a few minor bugs when I'm running morpheus version locally in Chromium. You does not specify protocol in the external datasets like CCLE and my browser tries to open them via file:// protocol and fails. See the scrennshot

Alexey

Hello,
There's a problem with numbers like '2.343e-10' in annotations, because they're visualized like '2.343e-1', you truncate zeros from the end of such numbers as well as from '0.001000'.

Dear authors,

Could you please kindly explain how you handles the missing values for tSNE analysis?

Thanks,
Woody

Steps to reproduce:

1. Open any example dataset (say, gene expresion for Acute Myeloid Leukemia).
2. Open File/Open menu. Go to preloaded tab.
3. Open any example dataset, again could be AML.

The heatmap doesn't look as neatly, as when opened from the start page.

Hi, I am trying to load a url based JSON. The JSON is generated on the fly upon hitting that url. However, Morpheus is not loading the JSON, and just giving a blank page. It looks like it is the same source as a page that works, but no error, nothing pops up.

<!DOCTYPE html>
<meta charset="utf-8">

<link rel="stylesheet" href="morpheus.js-master/css/morpheus-latest.min.css">
<script type="text/javascript" src="morpheus.js-master/js/morpheus-external-latest.min.js"></script>
<script src="morpheus.js-master/js/morpheus-latest.min.js"></script>

<body>
<noscript>
    <p>Please enable JavaScript</p>
</noscript>
<div id="vis"></div>

<script type="text/javascript">
    morpheus.Util.loadTrackingCode();
    window.onerror = function () {
        morpheus.FormBuilder.showInModal({
            title: 'Error',
            html: 'Oops, something went wrong. Please try again.'
        });
    };

    var searchString = window.location.search;
    if (searchString.length === 0) {
        searchString = window.location.hash;
    }
    var landingPage = new morpheus.LandingPage();
    landingPage.$el.prependTo($(document.body));
    if (searchString.length === 0) {
        landingPage.show();
    } else {
        searchString = searchString.substring(1);
        var keyValuePairs = searchString.split('&');
        var params = {};
        for (var i = 0; i < keyValuePairs.length; i++) {
            var pair = keyValuePairs[i].split('=');
            params[pair[0]] = decodeURIComponent(pair[1]);
        }
        if (params.json) {
            var options = JSON.parse(decodeURIComponent(params.json));
            landingPage.open(options);
        } else if (params.url) { // url to config
            var $loading = morpheus.Util.createLoadingEl();
            $loading.appendTo($('#vis'));
            morpheus.Util.getText(params.url).done(function (options) {
                if (typeof (options) === 'string') {
                    options = JSON.parse(options);
                }
                landingPage.open(options);
            }).fail(function (err) {
                console.log('Unable to get config file');
                landingPage.show();
            }).always(function () {
                $loading.remove();
            });

        } else {
            landingPage.show();
        }
    }
</script>

<script>
    if ((window.location.protocol === 'https:' || window.location.protocol === 'http:') &&
        'serviceWorker' in navigator) {
        navigator.serviceWorker
            .register('sw.js');
    }

</script>
</body>

Hi

Thank you for this great tool. I wonder if it is possible to configure morpheus to display Fit To Window view onload?
I tried using tools: [{"name": "Fit To Window"}], but the code assumed the action would have a gui and raises an error.

morpheus-latest.min.js:1 Uncaught (in promise) TypeError: action.gui is not a function
    at morpheus-latest.min.js:1
    at Function.m.each.m.forEach (morpheus-external-latest.min.js:20)
    at morpheus.HeatMap._init (morpheus-latest.min.js:1)
    at morpheus-latest.min.js:1

To reproduce:

1. Select "My computer" in "Open your own file" list, file selection dialog opens.
2. Cancel file selection.
3. Clicking "My computer" doesn't work.

I'm using chromium

The dotted line used to cut the row dendrogram tree literally touch the side of the browser, it is therefore impossible to use the mouse to click and drag it

Add a ward linkage option to hierarchical clustering

Hi,

In GENE-E there was a nice feature for importing row/column annotations from external files. Could you add it to morpheus?