GOTreeVis: Tree visualization for Gene Ontology enrichment results
In dottercp/GOTreeVis: Tree Visualization for Enrichment Results.

View source: R/GOTreeVis.R

GOTreeVis

R Documentation

Tree visualization for Gene Ontology enrichment results

Description

GOTreeVis creates a GOTree visualisation of GO enrichment data and writes it to a pdf file.

Usage

GOTreeVis(disp_data, out_file, b_rootlabel = "",
  b_sidelabels = c("GO:MF", "GO:BP"), b_parse = F,
  plot_pvalue_labels = T, root_color = "black",
  colors = c("deepskyblue3", "seagreen3"), oneside = NULL,
  font = "sans", pval_scaling = NA, br_spacing = NA, tr_width = 4,
  br_min_size = 2, br_max_size = 4, br_angle = 1/7,
  br_textoffset_x = 0, br_textoffset_y = 0, br_offset = NA,
  plot_size = 8, label_size = 4, expand_x = c(0.1, 0.1))

Arguments

`disp_data`	Enrichment data to visualize. Four columns: Term Pvalue - scales the length of the branches Count (i.e. number of genes matching the term) - scales the thickness of the branches. If this scaling is not needed, this column should be set to all equal values. All branches will then be set to min_size. a column used to determine the side of the tree, e.g. ontology (BP/MF). In case of a one-sided tree (see oneside parameter) the fourth column can be omitted. The side column should be a factor with two levels (first level = left, second = right). For character side columns a factor will be generated (levels will be in alphabetical order).
`out_file`	Filename of the output file. The name must end with a valid file extension to define the graphics device. PDF output is recommended.
`b_rootlabel`	Text for the label at the root of the tree. [default: ""]
`b_sidelabels`	Text for the labels on each side; The first value corresponds to the left side. [default: ('GO:MF','GO:BP')]
`b_parse`	Parse text for root and side labels using plotmath. Can be used to plot labels containing superscript or subscript.
`plot_pvalue_labels`	Should the p-value labels on the axis be plotted or not? [default: T]
`root_color`	Color for the 'root' box at the bottom of the tree. Applies to text and border. [default: black]
`colors`	Colors for the two sides of the tree, again first=left. [default: blue/green]
`oneside`	Special functionality in case only one category should be plotted.
`font`	Font family to be used for the text in the plot [default: sans]
`pval_scaling`	Scaling factor between -log(pvalue) and branch length; Gets generated automatically from the dimensions of the data if left unset (recommended for first run). Can be used to scale the tree in x dimension. [default: NA]
`br_spacing`	Spacing between branches. Gets generated automatically from the dimensions of the data if left unset (recommended for first run). Can be used to scale the tree in y dimension. [default: NA]
`tr_width`	Adjusts the width of the trunk. [default: 4]
`br_min_size`	Sets the count->branch_width scale. Defines the size(width) of the branch with the smallest count value. [default: 2]
`br_max_size`	Sets the count->branch_width scale. Defines the size(width) of the branch with the highest count value. [default: 4]
`br_angle`	Angle of the branches in radians as multiples of pi. [default: 1/7, equal to 180°/7]
`br_textoffset_x`	Manually offset the text from the branches (x-axis). [default: 0]
`br_textoffset_y`	Manually offset the text from the branches (y-axis). [default: 0]
`br_offset`	Adjust the position of the top branch (e.g. if the position should be at the very top). [default: scales with spacing]
`plot_size`	Plot size, passed to ggsave for both height and width; changes of this value will likely require adjustments of label_size. [default: 8]
`label_size`	Adjusts the font size of all labels in the plot. [default: 4]
`expand_x`	[default: (0.1,0.1)] can be used to expand the plot area on each side in case of long labels