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

---

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

---

Visualize pathway differences between two conditions

Description

Compute pathway-level comparison values from two symbol-keyed numeric vectors and render them through wp_bgfill().

Usage

wp_comparefill(
  p,
  value,
  control,
  mode = c("difference", "log2_ratio"),
  pseudocount = 1,
  high = "red",
  low = "blue",
  legend = TRUE,
  legend_x = 0.001,
  legend_y = 0.94
)

Arguments

p	A wpplot object.
value	Case-condition values.
control	Control-condition values.
mode	Comparison mode: direct difference or log2 ratio.
pseudocount	Added before ratio calculation when mode = "log2_ratio".
high	High-end color passed to wp_bgfill().
low	Low-end color passed to wp_bgfill().
legend	Whether to draw the legend.
legend_x	Horizontal position of the legend.
legend_y	Vertical position of the legend.

Value

A wpplot object.

---

Map user values to pathway symbols

Description

Normalize a named numeric vector or a data.frame into a symbol-keyed numeric vector that can be used by wp_bgfill().

Usage

wp_map(
  data,
  value_col = NULL,
  symbol_col = NULL,
  id_col = NULL,
  mapping = NULL,
  mapping_from = NULL,
  mapping_to = NULL,
  aggregator = c("mean", "median", "max_abs", "first", "sum"),
  na.rm = TRUE
)

Arguments

data	A named numeric vector or a data.frame.
value_col	Value column name when data is a data.frame.
symbol_col	Symbol column name when data already contains gene symbols.
id_col	Identifier column name when data needs ID mapping.
mapping	Optional ID-to-symbol mapping. It can be a named character vector or a two-column data.frame.
mapping_from	Source ID column in mapping when mapping is a data.frame.
mapping_to	Target symbol column in mapping when mapping is a data.frame.
aggregator	Aggregation rule used when multiple rows map to the same symbol.
na.rm	Whether to remove NA values before aggregation.

Value

A named numeric vector keyed by gene symbol.

---

Render one or more WikiPathways entries

Description

Render pathway IDs directly from a character vector, a result table, or an enrichment-like S4 object with a result slot.

Usage

wp_render(
  pathway,
  value = NULL,
  control = NULL,
  n = NULL,
  id_col = "ID",
  name_col = NULL,
  dir = NULL,
  file_ext = "png",
  filename_template = "{id}",
  width = NULL,
  height = NULL,
  shadowtext = FALSE,
  bg.r = 2,
  bg.col = "white",
  mode = c("difference", "log2_ratio"),
  pseudocount = 1,
  high = "red",
  low = "blue",
  legend = TRUE,
  legend_x = 0.001,
  legend_y = 0.94
)

Arguments

pathway	Pathway IDs, a data.frame, or an enrichment-like S4 object.
value	Optional symbol-keyed values for single-condition rendering.
control	Optional symbol-keyed control values for comparison rendering.
n	Maximum number of pathway IDs to render.
id_col	Column name that stores pathway IDs.
name_col	Optional column name used for output file naming when pathway is a data.frame or an enrichment-like result table.
dir	Optional output directory. When provided, PNG files are written there.
file_ext	Output file extension(s) passed to wpsave().
filename_template	Output filename template. Supported placeholders: {index}, {id}, and {name}.
width	Width passed to wpsave().
height	Height passed to wpsave().
shadowtext	Whether to add halo text after fill rendering.
bg.r	Halo width passed to wp_shadowtext().
bg.col	Halo color passed to wp_shadowtext().
mode	Comparison mode passed to wp_comparefill().
pseudocount	Pseudocount passed to wp_comparefill().
high	High-end color passed to fill functions.
low	Low-end color passed to fill functions.
legend	Whether to draw the legend.
legend_x	Horizontal position of the legend.
legend_y	Vertical position of the legend.

Value

A named list of wpplot objects.

---

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

## Not run: 
   wpplot('WP179') 

## End(Not run)

---

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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