FacetWP can be integrated with several WooCommerce Plugins:
Variation Swatches for WooCommerce by Emran Ahmed lets you attach colors or images to your WooCommerce product attributes.
With this plugin activated, you can use our Color add-on facet type to filter products by color.
When adding a color facet, set its Data Source to the product attribute containing your custom color / image swatch.
WooCommerce Attribute Swatches by IconicWP, a premium plugin that works similarly to Variation Swatches for WooCommerce (same setup instructions as above).