D3.zoom jumps when using mouse wheel after programmatically zoom

When I zoom to a specific location on a mouse click and then try to pan or when I'm using the mouse wheel, the zoom behavior jumps. It seems that my zoom level is being restored like it was before the mouse click.

Here is my event handler:

function click(d) {
    var x, y, k;

    if (d && centered !== d) {
       var centroid = path.centroid(d);
       x = centroid[0];
       y = centroid[1];
       k = 4;
       centered = d;
     } else {
       x = width / 2;
       y = height / 2;
       k = 1;
       centered = null;
    }


    svgContainer.transition()
       .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")scale(" + k + ")translate(" + -x + "," + -y + ")");
}

And this is how I "activate" my zoom and pan functionalities.

var svgContainer = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height)
    .call(d3.zoom().on("zoom", function () {
         svgContainer.attr("transform", d3.event.transform)
    }))
    .append("g")
    ...

svgContainer.selectAll(null)
    .data(feat.features)
    .enter()
    .append("path")
    .on("click", click)
     ...

Background

You are manipulating the transform applied to your elements in the click function but not updating the zoom state to reflect this. d3.zoom does not track an element's transform at all. So when you modify the transform attribute of an element independently of d3.zoom, d3.zoom no longer "knows" what the transform is of that element - it remains unchanged. D3.zoom does track zoom state - internally and independently of any element's transform attribute.

It might seem odd that d3.zoom doesn't track an element's transform, but there is good reason. d3.zoom isn't always used to manipulate the transform of an element, it may alter something like element width or a scale while that element's transform remains unchanged. Here's a bl.ock of mine where d3.zoom here manipulates only the radius of circles on canvas.

Problem

As you don't update the zoom state in your click event, d3.zoom picks up where it was last left when applying a new zoom event, which explains your symptom: "It seems that my zoom level being restored like it was before the mouse click."

Solution

So, what do you need to do? You need to pass your zoom transform to d3.zoom and trigger a zoom event. This way d3.zoom is apprised of the current zoom state. Luckily there is a method for this. We take a d3.zoomIdentity (k=1,x=0,y=0) and translate and scale as appropriate, we can translate, scale, and then translate again as you have done too:

   // Create a zoom transform from d3.zoomIdentity
   var transform = d3.zoomIdentity
    .translate(250,150)
    .scale(k)
    .translate(-x,-y);

And then we apply the zoom by calling zoom.transform which according to the docs:

sets the current zoom transform of the selected elements to the specified transform, instantaneously emitting start, zoom and end events. If selection is a transition, defines a “zoom” tween to the specified transform using d3.interpolateZoom, emitting a start event when the transition starts, zoom events for each tick of the transition, and then an end event when the transition ends (or is interrupted). (link)

We can call zoom.transform with:

   // Apply the zoom and trigger a zoom event with a provided zoom transform:
   svg.call(zoom.transform, transform);

So if this is analagous to what you have:

var zoom = d3.zoom()
  .scaleExtent([1,8])
  .translateExtent([[0,0],[500,300]])
  .on("zoom",zoomed);

var svg = d3.select("div")
  .append("svg")
  .attr("width",500)
  .attr("height",300)
  .call(zoom);
  
var g = svg.append("g");
  
var rects = g.selectAll(null)
  .data(d3.range(750))
  .enter()
  .append("rect")
  .attr("width",17)
  .attr("height",17)
  .attr("fill","#eee")
  .attr("y", function(d) { return Math.floor(d/50) * 20; })
  .attr("x", function(d) { return d%50 * 20; })
  .on("click", click);

function zoomed() {
  g.attr("transform", d3.event.transform);
}

function click(d) {
   rects.attr("fill","#eee");  
   
   var clicked = d3.select(this);
   clicked.attr("fill","orange");
   
   var x = +clicked.attr("x")+10;
   var y = +clicked.attr("y")+10;
   var k = 5;
   
   var transform = "translate(" + 250 + "," + 150 + ")scale(" + k + ")translate(" + -x + "," + -y + ")";
   
   g.transition()
     .attr("transform",transform)
     .duration(1000);
}

rect {
  stroke-width: 1px;
  stroke: #ccc;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/5.7.0/d3.min.js"></script>
<div>

This can be analagous to your solution:

var zoom = d3.zoom()
  .scaleExtent([1,8])
  .translateExtent([[0,0],[500,300]])
  .on("zoom",zoomed);

var svg = d3.select("div")
  .append("svg")
  .attr("width",500)
  .attr("height",300)
  .call(zoom);
  
var g = svg.append("g");
  
var rects = g.selectAll(null)
  .data(d3.range(750))
  .enter()
  .append("rect")
  .attr("width",17)
  .attr("height",17)
  .attr("fill","#eee")
  .attr("y", function(d) { return Math.floor(d/50) * 20; })
  .attr("x", function(d) { return d%50 * 20; })
  .on("click", click);

function zoomed() {
  g.attr("transform", d3.event.transform);
}

function click(d) {
   rects.attr("fill","#eee");  
   
   var clicked = d3.select(this);
   clicked.attr("fill","orange");
   
   var x = +clicked.attr("x")+10;
   var y = +clicked.attr("y")+10;
   var k = 5;

   // Create a zoom transform from d3.zoomIdentity
   var transform = d3.zoomIdentity
    .translate(250,150)
    .scale(k)
    .translate(-x,-y);
   
   // Apply the zoom and trigger a zoom event:
   svg.call(zoom.transform, transform);

}

rect {
  stroke-width: 1px;
  stroke: #ccc;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/5.7.0/d3.min.js"></script>
<div>