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I want to plot x-axis and y-axis with two measures in a scatterplot.
It works fine with one measure, but not with two.
How should I set it up?
(x-axis, y-axis, data1 as a bubble, data2 as a bubble)
The simplest form of scatter plot must have one dimension and two measures. The dimension defines how many data points you have, and the two measures define the coordinates (x and y axes) in the scatter chart.
So I don't understand what your scatter chart with one measure looks like. You need to give us more information about what you have done, and what you want to do.
See also https://community.qlik.com/t5/Design/Recipe-for-a-Scatter-Chart/ba-p/1468860. This blog post is for QlikView, but much of it is relevant for Qlik Sense also.