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I am trying to create a Web App, using the ArcGIS Online feature of downloading the javascript code, with the map id being used for connecting to the ArcGIS Online. I was able to do that successfully but the only issue is that I do not want a basemap. I only want the overlaying shapefile to be visible. How can I do that? Or is it not possible?

ArcGIS Online does provides an option, where I can make my shapefile as the basemap and then the features of popups cannot be used on it. Any ideas how I can work it out?

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Without looking at your code and knowing what end-result you're actually going for, I think the easiest solution is to just edit your JavaScript code and omit adding the basemap into your map object. Most basemap calls look like one of these two lines:

map.addLayer(basemap);
map.addLayers([basemap, myData, otherLayers, mapIsGettingCrowded]);

(Note the plural when adding more than one map)

Removing/editing whichever line is relevant should remove the basemap from your Web App.

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