pl_tracksplot

Instructions

tracksplot,compact plot of expression of a list of genes..

Input Schema

Name	Required	Description	Default
`color_map`	No	Color map to use for continuous variables.
`dendrogram`	No	If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added.
`figsize`	No	Figure size. Format is (width, height).
`gene_symbols`	No	Column name in .var DataFrame that stores gene symbols.
`groupby`	Yes	The key of the observation grouping to consider.
`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.
`palette`	No	Colors to use for plotting categorical annotation groups.
`use_raw`	No	Use raw attribute of adata if present.
`var_group_labels`	No	Labels for each of the var_group_positions that want to be highlighted.
`var_group_positions`	No	Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions.
`var_names`	No	var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values.
`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.

Input Schema (JSON Schema)

{
  "description": "Input schema for the tracksplot plotting tool.",
  "properties": {
    "color_map": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Color map to use for continuous variables.",
      "title": "Color Map"
    },
    "dendrogram": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "string"
        }
      ],
      "default": false,
      "description": "If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added.",
      "title": "Dendrogram"
    },
    "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"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        }
      ],
      "description": "The key of the observation grouping to consider.",
      "title": "Groupby"
    },
    "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"
    },
    "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"
    },
    "use_raw": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use raw attribute of adata if present.",
      "title": "Use Raw"
    },
    "var_group_labels": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Labels for each of the var_group_positions that want to be highlighted.",
      "title": "Var Group Labels"
    },
    "var_group_positions": {
      "anyOf": [
        {
          "items": {
            "maxItems": 2,
            "minItems": 2,
            "prefixItems": [
              {
                "type": "integer"
              },
              {
                "type": "integer"
              }
            ],
            "type": "array"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions.",
      "title": "Var Group Positions"
    },
    "var_names": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "additionalProperties": {
            "items": {
              "type": "string"
            },
            "type": "array"
          },
          "type": "object"
        }
      ],
      "default": null,
      "description": "var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values.",
      "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"
    }
  },
  "required": [
    "groupby"
  ],
  "title": "TracksplotModel",
  "type": "object"
}

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Instructions

Input Schema

Input Schema (JSON Schema)

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