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  "Title": "A Tidy Implementation of Heatmap",
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  "Description": "This is a tidy implementation for heatmap.  At the moment\nit is based on the (great) package 'ComplexHeatmap'.  The goal\nof this package is to interface a tidy data frame with this\npowerful tool.  Some of the advantages are: Row and/or columns\ncolour annotations are easy to integrate just specifying one\nparameter (column names).  Custom grouping of rows is easy to\nspecify providing a grouped tbl. For example: df %>%\ngroup_by(...).  Labels size adjusted by row and column total\nnumber.  Default use of Brewer and Viridis palettes.",
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    "annotation_point",
    "annotation_tile",
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    "get_heatmap_data",
    "heatmap",
    "layer_arrow_down",
    "layer_arrow_up",
    "layer_asterisk",
    "layer_diamond",
    "layer_point",
    "layer_square",
    "layer_star",
    "layer_text",
    "save_pdf",
    "scale_robust",
    "split_columns",
    "split_rows",
    "wrap_heatmap"
  ],
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    {
      "name": "N52",
      "title": "Example data set N52",
      "object": "N52",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Category",
        "symbol_ct",
        "symbol",
        "sample_ct",
        "Cell type",
        "inflection",
        "sample",
        "read count",
        "read count normalised",
        "TMM",
        "multiplier",
        "filt_for_calc",
        "CAPRA_TOTAL",
        "UBR",
        "read count normalised log"
      ],
      "rows": 520,
      "table": true,
      "tojson": true
    },
    {
      "name": "pasilla",
      "title": "Example data set Pasilla",
      "object": "pasilla",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample",
        "symbol",
        "count normalised adjusted",
        "condition",
        "type",
        "location",
        "activation",
        "count normalised adjusted log"
      ],
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      "table": true,
      "tojson": true
    }
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    {
      "page": "plus-.InputHeatmap",
      "title": "Add two tidyHeatmap objects together",
      "topics": [
        "+.InputHeatmap"
      ]
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      "page": "add_annotation",
      "title": "add_annotation",
      "topics": [
        "add_annotation"
      ]
    },
    {
      "page": "add_attr",
      "title": "Add attribute to abject",
      "topics": [
        "add_attr"
      ]
    },
    {
      "page": "add_class",
      "title": "Add class to abject",
      "topics": [
        "add_class"
      ]
    },
    {
      "page": "annot_to_list",
      "title": "annot_to_list",
      "topics": [
        "annot_to_list"
      ]
    },
    {
      "page": "annotation_bar-method",
      "title": "Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "annotation_bar",
        "annotation_bar,InputHeatmap-method"
      ]
    },
    {
      "page": "annotation_group",
      "title": "Add group annotation strips to a tidyHeatmap",
      "topics": [
        "annotation_group",
        "annotation_group,InputHeatmap-method"
      ]
    },
    {
      "page": "annotation_line-method",
      "title": "Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "annotation_line",
        "annotation_line,InputHeatmap-method"
      ]
    },
    {
      "page": "annotation_numeric-method",
      "title": "Adds a numeric annotation layer to an `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "annotation_numeric",
        "annotation_numeric,InputHeatmap-method"
      ]
    },
    {
      "page": "annotation_point-method",
      "title": "Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "annotation_point",
        "annotation_point,InputHeatmap-method"
      ]
    },
    {
      "page": "annotation_tile-method",
      "title": "Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "annotation_tile",
        "annotation_tile,InputHeatmap-method"
      ]
    },
    {
      "page": "as_ComplexHeatmap-method",
      "title": "Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g. changing legend position)",
      "topics": [
        "as_ComplexHeatmap",
        "as_ComplexHeatmap,InputHeatmap-method"
      ]
    },
    {
      "page": "as_matrix",
      "title": "Get matrix from tibble",
      "topics": [
        "as_matrix"
      ]
    },
    {
      "page": "check_if_duplicated_genes",
      "title": "Check whether there are duplicated genes/transcripts",
      "topics": [
        "check_if_duplicated_genes"
      ]
    },
    {
      "page": "check_if_wrong_input",
      "title": "Check whether there are NA counts",
      "topics": [
        "check_if_wrong_input"
      ]
    },
    {
      "page": "drop_class",
      "title": "Remove class to abject",
      "topics": [
        "drop_class"
      ]
    },
    {
      "page": "error_if_log_transformed",
      "title": "Check whether a numeric vector has been log transformed",
      "topics": [
        "error_if_log_transformed"
      ]
    },
    {
      "page": "get_abundance_norm_if_exists",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_abundance_norm_if_exists"
      ]
    },
    {
      "page": "get_elements",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_elements"
      ]
    },
    {
      "page": "get_elements_features",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_elements_features"
      ]
    },
    {
      "page": "get_elements_features_abundance",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_elements_features_abundance"
      ]
    },
    {
      "page": "get_heatmap_data-method",
      "title": "Retrieve heatmap data and dendrograms as plotted",
      "topics": [
        "get_heatmap_data",
        "get_heatmap_data,InputHeatmap-method"
      ]
    },
    {
      "page": "get_sample_counts",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_sample_counts"
      ]
    },
    {
      "page": "get_sample_transcript",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_sample_transcript"
      ]
    },
    {
      "page": "get_sample_transcript_counts",
      "title": "Get column names either from user or from attributes",
      "topics": [
        "get_sample_transcript_counts"
      ]
    },
    {
      "page": "get_x_y_annotation_columns",
      "title": "get_x_y_annotation_columns",
      "topics": [
        "get_x_y_annotation_columns"
      ]
    },
    {
      "page": "heatmap-method",
      "title": "Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "heatmap",
        "heatmap,tbl-method",
        "heatmap,tbl_df-method",
        "heatmap_"
      ]
    },
    {
      "page": "ifelse_pipe",
      "title": "This is a generalisation of ifelse that accepts an object and return an objects",
      "topics": [
        "ifelse_pipe"
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    },
    {
      "page": "ifelse2_pipe",
      "title": "This is a generalisation of ifelse that accepts an object and return an objects",
      "topics": [
        "ifelse2_pipe"
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      "title": "input_heatmap",
      "topics": [
        "input_heatmap"
      ]
    },
    {
      "page": "layer_arrow_down-method",
      "title": "Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_arrow_down",
        "layer_arrow_down,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_arrow_up-method",
      "title": "Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_arrow_up",
        "layer_arrow_up,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_asterisk-method",
      "title": "Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_asterisk",
        "layer_asterisk,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_diamond-method",
      "title": "Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_diamond",
        "layer_diamond,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_point-method",
      "title": "Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_point",
        "layer_point,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_square-method",
      "title": "Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_square",
        "layer_square,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_star-method",
      "title": "Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_star",
        "layer_star,InputHeatmap-method"
      ]
    },
    {
      "page": "layer_text-method",
      "title": "Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`",
      "topics": [
        "layer_text",
        "layer_text,InputHeatmap-method"
      ]
    },
    {
      "page": "N52",
      "title": "Example data set N52",
      "topics": [
        "N52"
      ]
    },
    {
      "page": "parse_formula",
      "title": ".formula parser",
      "topics": [
        "parse_formula"
      ]
    },
    {
      "page": "pasilla",
      "title": "Example data set Pasilla",
      "topics": [
        "pasilla"
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      "title": "From rlang deprecated",
      "topics": [
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      "page": "quo_names",
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      "page": "save_pdf-methods",
      "title": "Save plot on PDF file",
      "topics": [
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    },
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      "page": "save_pdf-Heatmap-method",
      "title": "save_pdf",
      "topics": [
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      "topics": [
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    },
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      "page": "select_closest_pairs",
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      "topics": [
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    {
      "page": "split-methods",
      "title": "Split the heatmap row-wise depending on the biggest branches in the cladogram.",
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        "split_rows",
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    {
      "page": "wrap_heatmap-method",
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  "_vignettes": [
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      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Overview of the tidyHeatmap package",
      "author": "Stefano Mangiola",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Citation",
        "Functions/utilities available",
        "Installation",
        "Contribution",
        "Input data frame",
        "Plotting",
        "Saving",
        "Clustering",
        "Grouping and splitting",
        "Custom palettes",
        "Multiple groupings and annotations",
        "Annotation types",
        "Annotation size",
        "Layer symbol",
        "Complex layer symbol example with colors",
        "Layer text",
        "Complex layer text example with colors",
        "Adding heatmap side-by-side",
        "Using patchwork to integrate across heatmaps and including ggplots",
        "ComplexHeatmap further styling",
        "Add cell borders",
        "Drop row clustering",
        "Reorder rows elements",
        "Size of dendrograms",
        "Size of rows/columns titles and names",
        "Remove row and column titles",
        "Align numeric annotation",
        "External ComplexHeatmap functionalities",
        "Chainging side of legends",
        "Add title using draw from ComplexHeatmap",
        "Add title using ggtitle from ggplot2",
        "Session Info"
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      "created": "2020-01-13 06:59:38",
      "modified": "2025-10-27 23:26:31",
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