Vega Heatmap

src/pyciemss/visuals/graphs.py

@@ -71,4 +71,10 @@ def spring_force_graph(
         labels = vega.find_named(schema["marks"], "labels")
         labels["encode"]["enter"]["text"]["field"] = f"datum.{node_labels}"
 
+    if not directed_graph:
+        schema["marks"] = vega.delete_named(schema["marks"], "arrows")
+
     return schema
+
+
+

src/pyciemss/visuals/histogram.py

@@ -81,3 +81,81 @@ def as_value_list(label, data):
         return schema, pd.DataFrame(desc).set_index(["bin0", "bin1"])
     else:
         return schema
+
+
+
+def heatmap_scatter(
+    data: pd.DataFrame,
+    x_name: str = "x_name",
+    y_name: str = "y_name",
+    x_bin: int = 10,
+    y_bin: int = 10
+) -> vega.VegaSchema:
+    """
+    **data -- Datasets as pandas dataframe, should contain x_name and y_name,
+    x_name: str name of column in dataset for x axis,
+    y_name: str, name of column in dataset for y axis,
+    x_bin: int = 10, max bins by x axis,
+    y_bin: int = 10, max bins by y axis,
+    """
+    json_dict = data.to_json(orient = 'records')
+    schema = vega.load_schema("heatmap_scatter.vg.json")
+
+    schema["data"] = vega.replace_named_with(schema["data"], "points", ["values"], json_dict)
+
+    schema["data"] = vega.replace_named_with(schema["data"], "source_0", ["values"], json_dict)
+
+    schema["signals"] = vega.replace_named_with(
+            schema["signals"], "bandwidthX", ["value"], x_bin
+        )
+    schema["signals"] = vega.replace_named_with(
+            schema["signals"], "bandwidthY", ["value"], y_bin
+        )
+    schema["signals"] = vega.replace_named_with(
+            schema["signals"], "x_name", ["value"], x_name
+        )
+
+    schema["signals"] = vega.replace_named_with(
+            schema["signals"], "y_name", ["value"], y_name
+        )
+
+    return schema
+
+
+
+def mesh_scatter(
+    mesh_data,
+    scatter_data: pd.DataFrame,
+) -> vega.VegaSchema:
+    """
+    **mesh_data -- input as mesh data, will be converted to grids
+    **scatter_data -- with alpha and gamma data
+    """
+
+    schema = vega.load_schema("mesh_scatter.vg.json")
+
+    def mesh_to_heatmap(mesh_data):
+        """
+        **mesh_data -- input as mesh data, will be converted to grids
+        adding half the difference in grid spacing to each coordinate 
+        so point becomes center of a grid for heatmap
+        """
+        xv, yv, zz = mesh_data
+        half_spacing_x = (xv[0, 1] - xv[0, 0])/2
+        half_spacing_y = (yv[1, 0] - yv[0, 0])/2
+        dataset = pd.DataFrame({"x_start": xv.ravel() - half_spacing_x, \
+                                "x_end": xv.ravel() + half_spacing_x, \
+                                    "y_start": yv.ravel() - half_spacing_y,     
+                                    "y_end": yv.ravel() + half_spacing_y,
+                                    '__count': zz.ravel()})
+        return dataset.to_json(orient="records")
+
+    # convert to json
+    json_heatmap = mesh_to_heatmap(mesh_data)
+    json_scatter = scatter_data.to_json(orient="records")
+
+    # update data in schema
+    schema["data"] = vega.replace_named_with(schema["data"], "points", ["values"], json_scatter)
+    schema["data"] = vega.replace_named_with(schema["data"], "mesh", ["values"], json_heatmap)
+
+    return schema

src/pyciemss/visuals/plots.py

@@ -9,7 +9,7 @@
 from .barycenter import triangle_contour
 from .trajectories import trajectories
 from .calibration import calibration
-from .histogram import histogram_multi
+from .histogram import histogram_multi, heatmap_scatter, mesh_scatter
 from .graphs import attributed_graph, spring_force_graph
 
 
@@ -26,6 +26,8 @@
     histogram_multi,
     attributed_graph,
     spring_force_graph,
+    heatmap_scatter,
+    mesh_scatter
 ]
 
 

src/pyciemss/visuals/schemas/heatmap_scatter.vg.json

@@ -0,0 +1,191 @@
+{
+  "$schema": "https://vega.github.io/schema/vega/v5.json",
+  "width": 300,
+  "height": 200,
+    "signals": [
+    {
+      "name": "bandwidthX", "value": 3,
+      "bind": {"input": "range", "min": 1, "max": 100, "step": 1}
+     },
+    {
+      "name": "bandwidthY", "value": 3,
+      "bind": {"input": "range", "min": 1, "max": 100, "step": 1}
+     },
+    { "name": "x_name", "value": "x_value",
+      "bind": {"input": "text"} 
+      },
+
+  { "name": "y_name", "value": "y_value",
+          "bind": {"input": "text"} 
+      }
+  ],
+  "data": [
+      {
+      "name": "points",
+      "values": [
+          {"x_value": 2, "y_value": 10},
+          {"x_value": 3, "y_value": 5},
+          {"x_value": 3, "y_value": 5},
+          {"x_value": 10, "y_value": 6},
+          {"x_value": 2, "y_value": 3},
+          {"x_value": 4, "y_value": 10},
+          {"x_value": 3, "y_value": 1}
+        ]
+      },
+    {
+      "name": "source_0",
+      "values": [
+          {"x_value": 2, "y_value": 10},
+          {"x_value": 3, "y_value": 5},
+          {"x_value": 3, "y_value": 5},
+          {"x_value": 2, "y_value": 3},
+          {"x_value": 4, "y_value": 10},
+          {"x_value": 3, "y_value": 1}
+        ],
+      "format": {"type": "json"},
+      "transform": [
+
+        {
+          "type": "extent",
+          "field": {"signal": "x_name"},
+          "signal": "x_extent"
+        },
+        {
+          "type": "bin",
+          "field": {"signal": "x_name"},
+          "as": [
+            "x_start",
+            "x_end"
+          ],
+          "signal": "x_bins",
+          "extent": {"signal": "x_extent"},
+          "maxbins": {"signal": "bandwidthX"}
+        },
+        {
+          "type": "extent",
+          "field": {"signal": "y_name"},
+          "signal": "y_extent"
+        },
+        {
+          "type": "bin",
+          "field": {"signal": "y_name"},
+          "as": [
+            "y_start",
+            "y_end"
+          ],
+          "signal": "y_bins",
+          "extent": {"signal": "y_extent"},
+          "maxbins": {"signal": "bandwidthY"}
+        },
+        {
+          "type": "aggregate",
+          "groupby": [
+            "x_start",
+            "x_end",
+            "y_start",
+            "y_end"
+          ],
+          "ops": ["count"],
+          "as": ["__count"]
+        }
+      ]
+    }
+  ],
+  "marks": [
+    {
+      "name": "marks",
+      "type": "rect",
+      "style": ["rect"],
+      "from": {"data": "source_0"},
+      "encode": {
+        "update": {
+          "fill": {"scale": "color", "field": "__count"},
+          "x2": {
+            "scale": "x",
+            "field": "x_start"
+          },
+          "x": {
+            "scale": "x",
+            "field": "x_end"
+          },
+          "y2": {
+            "scale": "y",
+            "field": "y_start"
+          },
+          "y": {
+            "scale": "y",
+            "field": "y_end"
+          }
+        }
+      }
+    },
+        {
+      "type": "symbol",
+      "from": {"data": "points"},
+      "encode": {
+        "enter": {
+          "fillOpacity": {"value": 1},
+          "fill": {"value": "black"}
+        },
+        "update": {
+          "x": {"scale": "x", "field" : {"signal": "x_name"}},
+          "y": {"scale": "y", "field" : {"signal": "y_name"}},
+          "size": {"value": 10}
+        }
+      }
+    }
+  ],
+  "scales": [
+    {
+      "name": "x",
+      "type": "linear",
+      "domain": {
+        "signal": "[x_bins.start, x_bins.stop]"
+      },
+      "range": [0, {"signal": "width"}],
+      "bins": {"signal": "x_bins"},
+      "zero": false
+    },
+    {
+      "name": "y",
+      "type": "linear",
+      "domain": {
+        "signal": "[y_bins.start, y_bins.stop]"
+      },
+      "range": [{"signal": "height"}, 0],
+      "bins": {"signal": "y_bins"},
+      "zero": false
+    },
+    {
+      "name": "color",
+      "type": "linear",
+      "domain": {"data": "source_0", "field": "__count"},
+      "range": "heatmap",
+      "interpolate": "hcl",
+      "zero": false
+    }
+  ],
+  "axes": [
+    {
+      "scale": "x",
+      "orient": "bottom",
+      "title": {"signal": "x_name"},
+      "labelOverlap": true,
+      "tickCount": {"signal": "ceil(width/3)"}
+    },
+    {
+      "scale": "y",
+      "orient": "left",
+      "title": {"signal": "y_name"},
+      "labelOverlap": true,
+      "tickCount": {"signal": "ceil(height/3)"}
+    }
+  ],
+  "legends": [
+    {
+      "fill": "color",
+      "gradientLength": {"signal": "height - 16"},
+      "title": "Count of Records"
+    }
+  ]
+}