visualifyjs 2.5.3-2.dev → 2.5.3-9-dev

package/docs/{docs/components → components}/plotly.md

@@ -1,62 +1,62 @@
-# Plotly Component
-
-The Plotly component is used to display a plotly plot on the page.
-
-## Properties
-
-The Plotly component has the following properties:
-
--   `type` (string): The type of the component, in this case `Plotly`.
--   `id` (string): The unique identifier of the component.
--   `row` (int): The row in which the component is to be displayed.
--   `col` (int): The column in which the component is to be displayed.
--   `rowspan` (int): The number of rows the component is to span.
--   `colspan` (int): The number of columns the component is to span.
--   `settings` (object): The settings of the component.
--   `parser` (object): The parser of the component.
--   `trigger` (object): The trigger of the component.
-
-### settings Properties
-
-The `settings` object has the following properties:
-
--   `preset` (string): The preset of the component.
--   `ignoreEmptyData` (boolean): Whether to ignore empty data or not.
-
-### parser Properties
-
-The `parser` object has the following properties:
-
--   `sources` (array): The sources of the component.
-    -   `name` (string): The name of the trigger.
-    -   `url` (string): The URL of the data.
-    -   `responseKey` (string): The response key of the component.
--   `exclude` (array): The data to be excluded.
--   `type` (string): The type of the component.
-
-### Example
-
-```json
-        {
-            "id": "mmtrbc_tsne",
-            "type": "Plotly",
-            "col": 2,
-            "rowspan": 3,
-            "settings": {
-                "preset": "mmtrbc",
-                "ignoreEmptyData": true
-            },
-            "parser": {
-                "sources": [{
-                    "name": "metadata",
-                    "url": "<your-backend-url>"
-                }, {
-                    "name": "gene",
-                    "url": "<your-backend-url>",
-                    "responseKey": "gene"
-                }],
-                "exclude": ["BC-Mes", "BC-NE", "BC-Im"],
-                "type": "scatter"
-            }
-        }
-```
+# Plotly Component
+
+The Plotly component is used to display a plotly plot on the page.
+
+## Properties
+
+The Plotly component has the following properties:
+
+-   `type` (string): The type of the component, in this case `Plotly`.
+-   `id` (string): The unique identifier of the component.
+-   `row` (int): The row in which the component is to be displayed.
+-   `col` (int): The column in which the component is to be displayed.
+-   `rowspan` (int): The number of rows the component is to span.
+-   `colspan` (int): The number of columns the component is to span.
+-   `settings` (object): The settings of the component.
+-   `parser` (object): The parser of the component.
+-   `trigger` (object): The trigger of the component.
+
+### settings Properties
+
+The `settings` object has the following properties:
+
+-   `preset` (string): The preset of the component.
+-   `ignoreEmptyData` (boolean): Whether to ignore empty data or not.
+
+### parser Properties
+
+The `parser` object has the following properties:
+
+-   `sources` (array): The sources of the component.
+    -   `name` (string): The name of the trigger.
+    -   `url` (string): The URL of the data.
+    -   `responseKey` (string): The response key of the component.
+-   `exclude` (array): The data to be excluded.
+-   `type` (string): The type of the component.
+
+### Example
+
+```json
+        {
+            "id": "mmtrbc_tsne",
+            "type": "Plotly",
+            "col": 2,
+            "rowspan": 3,
+            "settings": {
+                "preset": "mmtrbc",
+                "ignoreEmptyData": true
+            },
+            "parser": {
+                "sources": [{
+                    "name": "metadata",
+                    "url": "<your-backend-url>"
+                }, {
+                    "name": "gene",
+                    "url": "<your-backend-url>",
+                    "responseKey": "gene"
+                }],
+                "exclude": ["BC-Mes", "BC-NE", "BC-Im"],
+                "type": "scatter"
+            }
+        }
+```

package/docs/{docs/components → components}/scatterL.md

@@ -1,70 +1,70 @@
-# ScatterL Components
-
-The ScatterL component is a scatter plot that is used to visualize the data in
-2D. It is a part of the Plotly library and is used to visualize the data in 2D.
-The ScatterL component is used to visualize the data in 2D.
-
-The ScatterL component is designed for a specified data Format, like R-tree, to
-visualize a large data set in 2D.
-
-## Requirements
-
-The ScatterL component requires the specified API to fetch the data. Currently,
-the ScatterL component supports the API for fetching the data - in the format of
-JSON, - and it need API to consist as
-`your-backend-server-url/xxx/<x-min>/<y-min>/<x-max>/<y-max>`
-
-We will provide an example of the backend to show you how to implement our
-customized Rtree API.
-
-## Properties
-
-The ScatterL component has the following properties:
-
--   `type` (string): The type of the component, in this case `ScatterL`.
--   `id` (string): The unique identifier of the component.
--   `row` (int): The row in which the component is to be displayed.
--   `col` (int): The column in which the component is to be displayed.
--   `rowspan` (int): The number of rows the component is to span.
--   `config` (object): The configuration of the component.
-
-### config Properties
-
-The `config` object has the following properties:
-
--   `merge` (boolean): Whether to merge the data or not.
--   `startup_msg` (string): The message to be displayed when the component is
-    started.
--   `size` (object): The size of the component.
-    -   `width` (int): The width of the component.
-    -   `height` (int): The height of the component.
-    -   `dotsize` (object): The size of the dots in the scatter plot.
-    -   `dotFactor` (int): The factor by which the dot size is to be multiplied.
-        -   `min` (int): The minimum size of the dot.
-        -   `max` (int): The maximum size of the dot.
-    -   `colourby` (string): The property by which the dots are to be coloured.
-    -   `exclusion` (array): The properties to be excluded.
-    -   `api` (object): The API to be used to fetch the data.
-        -   `metadata` (object): The metadata API.
-            -   `href` (string): The URL of the metadata API.
-            -   `val` (string): The value of the metadata API.
-        -   `gene` (object): The gene API.
-            -   `href` (string): The URL of the gene API.
-            -   `val` (string): The value of the gene API.
-            -   `dep` (string): The dependent property of the gene API.
-    -   `mapping` (object): The mapping of the data.
-        -   `api` (object): The API to be used for mapping.
-            -   Example:
-                -   `ENS (S): 'ens_iter_2'` (string): Maps ENS (S) to endo_iter_2 API.
-                -   `IM (S): 'im_iter_2'` (string): Maps IM (S) to im_iter_2 API.
-                -   `MES (S): 'mes_iter_2'` (string): Maps MES (S) to mes_iter_2 API.
-        -   `axis` (object): The axis to be used for mapping.
-            -   `x: X_Coord` (string):  Maps x-axis to specified value name.
-            -   `y: Y_Coord` (string): Maps y-axis to specified value name.
-            -   `extra` (object): The extra properties.
-                -   Example:
-                    -   `Stage : Stage` (string): Mapes the Stage to the stage property.
-                    -   `MT : MT` (string): Maps the MT to the MT property.
-                    -   `Gene : Gene` (string): Maps the Gene to the gene property.
-                    -   `Cell_Type : Cell_Type` (string): Maps the Cell_Type to the cell type property.
-                    -   `Cell_ID : Cell_ID` (string): Maps the Cell_ID to the cell ID property.
+# ScatterL Components
+
+The ScatterL component is a scatter plot that is used to visualize the data in
+2D. It is a part of the Plotly library and is used to visualize the data in 2D.
+The ScatterL component is used to visualize the data in 2D.
+
+The ScatterL component is designed for a specified data Format, like R-tree, to
+visualize a large data set in 2D.
+
+## Requirements
+
+The ScatterL component requires the specified API to fetch the data. Currently,
+the ScatterL component supports the API for fetching the data - in the format of
+JSON, - and it need API to consist as
+`your-backend-server-url/xxx/<x-min>/<y-min>/<x-max>/<y-max>`
+
+We will provide an example of the backend to show you how to implement our
+customized Rtree API.
+
+## Properties
+
+The ScatterL component has the following properties:
+
+-   `type` (string): The type of the component, in this case `ScatterL`.
+-   `id` (string): The unique identifier of the component.
+-   `row` (int): The row in which the component is to be displayed.
+-   `col` (int): The column in which the component is to be displayed.
+-   `rowspan` (int): The number of rows the component is to span.
+-   `config` (object): The configuration of the component.
+
+### config Properties
+
+The `config` object has the following properties:
+
+-   `merge` (boolean): Whether to merge the data or not.
+-   `startup_msg` (string): The message to be displayed when the component is
+    started.
+-   `size` (object): The size of the component.
+    -   `width` (int): The width of the component.
+    -   `height` (int): The height of the component.
+    -   `dotsize` (object): The size of the dots in the scatter plot.
+    -   `dotFactor` (int): The factor by which the dot size is to be multiplied.
+        -   `min` (int): The minimum size of the dot.
+        -   `max` (int): The maximum size of the dot.
+    -   `colourby` (string): The property by which the dots are to be coloured.
+    -   `exclusion` (array): The properties to be excluded.
+    -   `api` (object): The API to be used to fetch the data.
+        -   `metadata` (object): The metadata API.
+            -   `href` (string): The URL of the metadata API.
+            -   `val` (string): The value of the metadata API.
+        -   `gene` (object): The gene API.
+            -   `href` (string): The URL of the gene API.
+            -   `val` (string): The value of the gene API.
+            -   `dep` (string): The dependent property of the gene API.
+    -   `mapping` (object): The mapping of the data.
+        -   `api` (object): The API to be used for mapping.
+            -   Example:
+                -   `ENS (S): 'ens_iter_2'` (string): Maps ENS (S) to endo_iter_2 API.
+                -   `IM (S): 'im_iter_2'` (string): Maps IM (S) to im_iter_2 API.
+                -   `MES (S): 'mes_iter_2'` (string): Maps MES (S) to mes_iter_2 API.
+        -   `axis` (object): The axis to be used for mapping.
+            -   `x: X_Coord` (string):  Maps x-axis to specified value name.
+            -   `y: Y_Coord` (string): Maps y-axis to specified value name.
+            -   `extra` (object): The extra properties.
+                -   Example:
+                    -   `Stage : Stage` (string): Mapes the Stage to the stage property.
+                    -   `MT : MT` (string): Maps the MT to the MT property.
+                    -   `Gene : Gene` (string): Maps the Gene to the gene property.
+                    -   `Cell_Type : Cell_Type` (string): Maps the Cell_Type to the cell type property.
+                    -   `Cell_ID : Cell_ID` (string): Maps the Cell_ID to the cell ID property.

package/docs/{docs/components → components}/visium.md

@@ -1,57 +1,57 @@
-# Visium Component
-
-The Visium component is used to display the Visium data on the page.
-
-## Properties
-
-The Visium component has the following properties:
-
--   `type` (string): The type of the component, in this case `Visium`.
--   `id` (string): The unique identifier of the component.
--   `row` (int): The row in which the component is to be displayed.
--   `col` (int): The column in which the component is to be displayed.
--   `rowspan` (int): The number of rows the component is to span.
--   `startup_msg` (string): The startup message of the component.
--   `meta` (string): The metadata API of the component.
--   `simpleload` (boolean): Whether to load the data simply or not.
--   `metaval` (string): The metadata variable name we want to use.
--   `gene` (string): The gene API.
--   `geneval` (string): The gene variable name we want to use.
--   `image` (string): The image API.
--   `cellval` (string): The celltype variable name we want to use.
--   `axis_mapping` (object): The axis mapping of the component.
-    -   `x: X_Coord` (string): Maps the X_Coord to the x-axis.
-    -   `y: Y_Coord` (string): Maps the Y_Coord to the y-axis.
-    -   `extra` (object): The extra properties.
-        -   Example:
-            -   `BC : BC` (string): Maps the BC to the BC property.
-            -   `SB-1 : SB-1` (string): Maps the SB-1 to the SB-1 property.
-
-
-### Example
-
-```json
-        {
-            "id": "visium_scatter2d",
-            "type": "Visium",
-            "row": 1,
-            "col": 2,
-            "rowspan": 3,
-            "startup_msg": "Section",
-            "meta": "<your-api-for-metadata>",
-            "simpleload": false,
-            "metaval": "visium_section",
-            "gene": "<your-api-for-gene-data>",
-            "geneval": "visium_gene",
-            "image": "<your-api-for-image>",
-            "cellval": "visium_celltype",
-            "axis_mapping": {
-                "x": "X_Coord",
-                "y": "Y_Coord",
-                "extra": {
-                    "BC": "BC",
-                    "SB-1": "SB-1",
-                }
-            }
-        }
+# Visium Component
+
+The Visium component is used to display the Visium data on the page.
+
+## Properties
+
+The Visium component has the following properties:
+
+-   `type` (string): The type of the component, in this case `Visium`.
+-   `id` (string): The unique identifier of the component.
+-   `row` (int): The row in which the component is to be displayed.
+-   `col` (int): The column in which the component is to be displayed.
+-   `rowspan` (int): The number of rows the component is to span.
+-   `startup_msg` (string): The startup message of the component.
+-   `meta` (string): The metadata API of the component.
+-   `simpleload` (boolean): Whether to load the data simply or not.
+-   `metaval` (string): The metadata variable name we want to use.
+-   `gene` (string): The gene API.
+-   `geneval` (string): The gene variable name we want to use.
+-   `image` (string): The image API.
+-   `cellval` (string): The celltype variable name we want to use.
+-   `axis_mapping` (object): The axis mapping of the component.
+    -   `x: X_Coord` (string): Maps the X_Coord to the x-axis.
+    -   `y: Y_Coord` (string): Maps the Y_Coord to the y-axis.
+    -   `extra` (object): The extra properties.
+        -   Example:
+            -   `BC : BC` (string): Maps the BC to the BC property.
+            -   `SB-1 : SB-1` (string): Maps the SB-1 to the SB-1 property.
+
+
+### Example
+
+```json
+        {
+            "id": "visium_scatter2d",
+            "type": "Visium",
+            "row": 1,
+            "col": 2,
+            "rowspan": 3,
+            "startup_msg": "Section",
+            "meta": "<your-api-for-metadata>",
+            "simpleload": false,
+            "metaval": "visium_section",
+            "gene": "<your-api-for-gene-data>",
+            "geneval": "visium_gene",
+            "image": "<your-api-for-image>",
+            "cellval": "visium_celltype",
+            "axis_mapping": {
+                "x": "X_Coord",
+                "y": "Y_Coord",
+                "extra": {
+                    "BC": "BC",
+                    "SB-1": "SB-1",
+                }
+            }
+        }
 ```

package/docs/{docs/configuration.md → configuration.md}

@@ -1,121 +1,123 @@
-# Configuration
-
-You can configure Visualify by defining `window.$visualify` or `$visualify` as
-an object:
-
-```js
-<script>
-window.$visualify = {
-    mode: 'pages',
-    // ...
-}
-</script>
-```
-
-Or you can initialize `$visualify` as a **Chart Module**:
-
-```js
-<script>
-$visualify = {
-    mode: 'charts',
-}
-
-new $visualify.Recharts({...}).mount('#chart')
-new $visualify.LiveEditor({...}).mount('#ex11');
-</script>
-```
-
-## el
-
--   Type: `String`
--   Default: `'#root'`
-
-The DOM element to be mounted on initialization. It can be a CSS selector string
-or an actual
-[HTMLElement](https://developer.mozilla.org/en-US/docs/Web/API/HTMLElement).
-
-```js
-window.$visualify = {
-  el: '#root',
-};
-```
-
-## mode
-
--   Type: `String`
--   Default: `'pages'`
--   Options: `'pages'`, `'charts'`
-
-The mode of Visualify. If you want to use Visualify as a chart module, you can
-set `mode` to `'charts'`.
-
-```js
-window.$visualify = {
-  mode: 'charts',
-};
-```
-
-## theme
-
--   Type: `String`
--   Default: `'modern'`
--   Options: `'modern'`, `'classic'`
-
-The theme of Visualify. The default theme is `'modern'`. Themes usually make
-changes to the layout and components of the page. Built-in different themes
-provide different typesetting and functions, please choose different themes
-according to different needs, you can also replace a single css to change the
-style.
-
-```js
-window.$visualify = {
-  theme: 'modern',
-};
-```
-
-For more themes, please refer to [Themes](themes.md)
-
-## homepage
-
--   Type: `String`
--   Default: `'home.json'`
-
-The `home.json` in your docs folder will be treated as the homepage for your
-website, but sometimes you may need to serve another file as your homepage.
-
-```js
-window.$visualify = {
-    homepage: 'home',
-
-    // Or use the json in your repo
-    homepage: 'https://raw.githubusercontent.com/leolihao/visualify/master/docs/home.json',
-}
-```
-
-## repo
-
--   Type: `String`
-
-Configure the repository url, or a string of `username/repo`, to add the
-[GitHub Corner](http://tholman.com/github-corners/) widget in the top right
-corner of the site.
-
-```js
-window.$docsify = {
-  repo: 'https://github.com/visualify',
-};
-```
-
-## alias
-
--   Type: `Object`
-
-Set the route alias. You can freely manage `routing` rules. Supports `RegExp`.
-
-```js
-window.$visualify = {
-  alias: {
-    '/docsify': 'https://docsify.js.org/#/configuration?id=alias',
-  },
-};
-```
+# Configuration
+
+You can configure Visualify by defining `window.$visualify` or `$visualify` as
+an object:
+
+```js
+<script>
+window.$visualify = {
+    mode: 'pages',
+    // ...
+}
+</script>
+```
+
+Or you can initialize `$visualify` as a **Chart Module**:
+
+```js
+<script>
+$visualify = {
+    mode: 'charts',
+}
+
+new $visualify.Recharts({...}).mount('#chart')
+new $visualify.LiveEditor({...}).mount('#ex11');
+</script>
+```
+
+## el
+
+-   Type: `String`
+-   Default: `'#root'`
+
+The DOM element to be mounted on initialization. It can be a CSS selector string
+or an actual
+[HTMLElement](https://developer.mozilla.org/en-US/docs/Web/API/HTMLElement).
+
+```js
+window.$visualify = {
+  el: '#root',
+};
+```
+
+## mode
+
+-   Type: `String`
+-   Default: `'pages'`
+-   Options: `'pages'`, `'charts'`
+
+The mode of Visualify. If you want to use Visualify as a chart module, you can
+set `mode` to `'charts'`.
+
+```js
+window.$visualify = {
+  mode: 'charts',
+};
+```
+
+## theme
+
+-   Type: `String`
+-   Default: `'modern'`
+-   Options: `'modern'`, `'classic'`
+
+The theme of Visualify. The default theme is `'modern'`. Themes usually make
+changes to the layout and components of the page. Built-in different themes
+provide different typesetting and functions, please choose different themes
+according to different needs, you can also replace a single css to change the
+style.
+
+```js
+window.$visualify = {
+  theme: 'modern',
+};
+```
+
+For more themes, please refer to [Themes](themes.md)
+
+## homepage
+
+-   Type: `String`
+-   Default: `'home.json'`
+
+The `home.json` in your docs folder will be treated as the homepage for your
+website, but sometimes you may need to serve another file as your homepage.
+
+```js
+window.$visualify = {
+    homepage: 'home',
+
+    // Or use the json in your repo
+    homepage: 'https://raw.githubusercontent.com/leolihao/visualify/master/docs/home.json',
+}
+```
+
+## repo
+
+-   Type: `String`
+
+Configure the repository url, or a string of `username/repo`, to add the
+[GitHub Corner](http://tholman.com/github-corners/) widget in the top right
+corner of the site.
+
+```js
+window.$docsify = {
+  repo: 'leolihao/visualify',
+  // or
+  repo: 'https://github.com/leolihao/visualify/',
+};
+```
+
+## alias
+
+-   Type: `Object`
+
+Set the route alias. You can freely manage `routing` rules. Supports `RegExp`.
+
+```js
+window.$visualify = {
+  alias: {
+    '/docsify': 'https://docsify.js.org/#/configuration?id=alias',
+  },
+};
+```