pl_violin

Instructions

Plot violin plot of one or more variables.

Input Schema

Name	Required	Description	Default
`color_map`	No	Color map to use for continuous variables.
`figsize`	No	Figure size. Format is (width, height).
`gene_symbols`	No	Column name in .var DataFrame that stores gene symbols.
`groupby`	No	The key of the observation grouping to consider.
`jitter`	No	Add jitter to the stripplot (only when stripplot is True).
`keys`	Yes	Keys for accessing variables of .var_names or fields of .obs.
`layer`	No	Name of the AnnData object layer that wants to be plotted.
`legend_fontoutline`	No	Line width of the legend font outline in pt.
`legend_fontsize`	No	Numeric size in pt or string describing the size.
`legend_fontweight`	No	Legend font weight. A numeric value in range 0-1000 or a string.	bold
`legend_loc`	No	Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter.	right margin
`log`	No	Plot on logarithmic axis.
`multi_panel`	No	Display keys in multiple panels also when groupby is not None.
`order`	No	Order in which to show the categories.
`palette`	No	Colors to use for plotting categorical annotation groups.
`rotation`	No	Rotation of xtick labels.
`scale`	No	The method used to scale the width of each violin.	width
`size`	No	Size of the jitter points.
`stripplot`	No	Add a stripplot on top of the violin plot.
`use_raw`	No	Use raw attribute of adata if present.
`var_names`	No	var_names should be a valid subset of adata.var_names.
`vcenter`	No	The value representing the center of the color scale.
`vmax`	No	The value representing the upper limit of the color scale.
`vmin`	No	The value representing the lower limit of the color scale.
`xlabel`	No	Label of the x axis. Defaults to groupby if rotation is None, otherwise, no label is shown.
`ylabel`	No	Label of the y axis.

Input Schema (JSON Schema)

{
  "description": "Input schema for the violin plotting tool.",
  "properties": {
    "color_map": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Color map to use for continuous variables.",
      "title": "Color Map"
    },
    "figsize": {
      "anyOf": [
        {
          "maxItems": 2,
          "minItems": 2,
          "prefixItems": [
            {
              "type": "number"
            },
            {
              "type": "number"
            }
          ],
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Figure size. Format is (width, height).",
      "title": "Figsize"
    },
    "gene_symbols": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Column name in .var DataFrame that stores gene symbols.",
      "title": "Gene Symbols"
    },
    "groupby": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The key of the observation grouping to consider.",
      "title": "Groupby"
    },
    "jitter": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "boolean"
        }
      ],
      "default": true,
      "description": "Add jitter to the stripplot (only when stripplot is True).",
      "title": "Jitter"
    },
    "keys": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        }
      ],
      "description": "Keys for accessing variables of .var_names or fields of .obs.",
      "title": "Keys"
    },
    "layer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Name of the AnnData object layer that wants to be plotted.",
      "title": "Layer"
    },
    "legend_fontoutline": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Line width of the legend font outline in pt.",
      "title": "Legend Fontoutline"
    },
    "legend_fontsize": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "number"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Numeric size in pt or string describing the size.",
      "title": "Legend Fontsize"
    },
    "legend_fontweight": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "string"
        }
      ],
      "default": "bold",
      "description": "Legend font weight. A numeric value in range 0-1000 or a string.",
      "title": "Legend Fontweight"
    },
    "legend_loc": {
      "default": "right margin",
      "description": "Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter.",
      "title": "Legend Loc",
      "type": "string"
    },
    "log": {
      "default": false,
      "description": "Plot on logarithmic axis.",
      "title": "Log",
      "type": "boolean"
    },
    "multi_panel": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Display keys in multiple panels also when groupby is not None.",
      "title": "Multi Panel"
    },
    "order": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Order in which to show the categories.",
      "title": "Order"
    },
    "palette": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "type": "string"
          },
          "type": "object"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Colors to use for plotting categorical annotation groups.",
      "title": "Palette"
    },
    "rotation": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Rotation of xtick labels.",
      "title": "Rotation"
    },
    "scale": {
      "default": "width",
      "description": "The method used to scale the width of each violin.",
      "enum": [
        "area",
        "count",
        "width"
      ],
      "title": "Scale",
      "type": "string"
    },
    "size": {
      "default": 1,
      "description": "Size of the jitter points.",
      "exclusiveMinimum": 0,
      "title": "Size",
      "type": "integer"
    },
    "stripplot": {
      "default": true,
      "description": "Add a stripplot on top of the violin plot.",
      "title": "Stripplot",
      "type": "boolean"
    },
    "use_raw": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use raw attribute of adata if present.",
      "title": "Use Raw"
    },
    "var_names": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "var_names should be a valid subset of adata.var_names.",
      "title": "Var Names"
    },
    "vcenter": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "number"
        },
        {
          "items": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "number"
              }
            ]
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The value representing the center of the color scale.",
      "title": "Vcenter"
    },
    "vmax": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "number"
        },
        {
          "items": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "number"
              }
            ]
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The value representing the upper limit of the color scale.",
      "title": "Vmax"
    },
    "vmin": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "number"
        },
        {
          "items": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "number"
              }
            ]
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The value representing the lower limit of the color scale.",
      "title": "Vmin"
    },
    "xlabel": {
      "default": "",
      "description": "Label of the x axis. Defaults to groupby if rotation is None, otherwise, no label is shown.",
      "title": "Xlabel",
      "type": "string"
    },
    "ylabel": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Label of the y axis.",
      "title": "Ylabel"
    }
  },
  "required": [
    "keys"
  ],
  "title": "ViolinModel",
  "type": "object"
}

SCMCP

Instructions

Input Schema

Input Schema (JSON Schema)

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