create_report {hipathia} | R Documentation

## Create visualization HTML

### Description

Saves the results of a Wilcoxon comparison for the Hipathia pathway values into a folder, and creates a HTML from which to visualize the results on top of the pathways. The results are stored into the specified folder. If this folder does not exist, it will be created. The parent folder must exist.

### Usage

    create_report(
      comp,
      metaginfo,
      output_folder = NULL,
      path = NULL,
      node_colors = NULL,
      group_by = "pathway",
      conf = 0.05,
      verbose = FALSE
    )

### Arguments

`comp` | Comparison object as given by the `do_wilcoxon` function
`metaginfo` | Pathways object as returned by the `load_pathways` function
`output_folder` | Name of the folder in which the report will be stored.
`path` | Absolute path to the parent directory in which 'output_folder' will be saved. If it is not provided, it will be created in a temp folder.
`node_colors` | List of colors with which to paint the nodes of the pathways, as returned by the `node_color_per_de` function. Default is white.
`group_by` | How to group the subpathways to be visualized. By default they are grouped by the pathway to which they belong. Available groupings include "uniprot", to group subpathways by their annotated Uniprot functions, "GO", to group subpathways by their annotated GO terms, and "genes", to group subpathways by the genes they include. Default is set to "pathway".
`conf` | Level of significance. By default 0.05.
`verbose` | Boolean, whether to show details about the results of the execution

### Value

Saves the results and creates a report to visualize them through a server in the specified `output_folder`. Returns the folder where the report has been stored.

### Examples

    data(comp)
    pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
    "hsa04012"))
    report <- create_report(comp, pathways, "save_results")

    ## Not run:
    data(results)
    data(brca)
    sample_group <- colData(brca)[,1]
    colors_de <- node_color_per_de(results, pathways,
    sample_group, "Tumor", "Normal")
    report_colors <- create_report(comp, pathways, "save_results",
    node_colors = colors_de)

    ## End(Not run)

[Package hipathia version 2.2.1 Index]