You can add Plausible Analytics tracking code to your Shopify website by editing the code in your theme file.
Go to the edit code section of your Shopify theme by clicking on "Online Store" in the left hand sidebar, then choose "Themes", click on the "Actions" button next to your current theme and choose the "Edit Code" option.
In the "Layout" section of the theme code editor select
Paste your Plausible Analytics script tag before the closing
</head>tag of the
theme.liquidfile and save it.
Now you can go to your website and verify whether Plausible Analytics script has been added and to your Plausible Analytics account to see whether the stats are being tracked. See here how to verify the integration.