Package 'wikiprofiler'

read.wp

Description

parse wikipathway gmt file to a gson object

Usage

read.wp(file)

Arguments

file	wikipathway gmt file downloaded from 'https://wikipathways-data.wmcloud.org/current/gmt/'

Value

a 'gson' object

Author(s)

Guangchuang Yu

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Fill the background of gene with color according to amount of gene expression.

Description

Generate a color array.Fill the gene then generate the legend.

Usage

wp_bgfill(
  p,
  value,
  high = "red",
  low = "blue",
  legend = TRUE,
  legend_x = 0.001,
  legend_y = 0.94
)

Arguments

p	p is
value	value is the amount of expression.
high	The color of highest gene.
low	The color of lowest gene.
legend	Whether you need legend.
legend_x	horizontal position of the legend
legend_y	vertical position of the legend

Value

A 'wpplot' object

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Add halo above gene name to get a clear view.

Description

Add use svghalo2 function to add halo.

Usage

wp_shadowtext(p, bg.r = 2, bg.col = "white")

Arguments

p	An wpplot class variance.
bg.r	The width of halo.
bg.col	The color of halo.

Value

A 'wpplot' object

---

Input specific wikipathways ID to get an output in class of wpplot.

Description

Use wikipathways ID to open a local svg file. Then extract related information from svg file and build a wpplot class variance.

Usage

wpplot(ID)

Arguments

ID	ID is wikipathways' ID.

Value

A 'wpplot' object

Examples

if (yulab.utils::has_internet())
   wpplot('WP179')

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Save the 'wpplot' object to a file.

Description

Save the 'wpplot' object to a file.

Usage

wpsave(p, file, width = NULL, height = NULL, ...)

Arguments

p	A 'wpplot' object
file	the file to save the object
width	Width of the figure
height	Height of the figure
...	additional parameter passed to 'ggsave'

Value

output the file and the input 'wpplot' object (invisible)

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