| Type: | Package |
| Title: | 'WikiPathway' Based Data Integration and Visualization |
| Version: | 0.1.6 |
| Description: | Queries online 'WikiPathway' graphics and allows mapping user data (e.g., expression values) on the graph. The package designs a grammar of graphic syntax that using pipe operator to add graphic layer. |
| Imports: | ggplot2, ggplotify, grDevices, grid, gson, rsvg, yulab.utils (≥ 0.1.7) |
| ByteCompile: | true |
| License: | Artistic-2.0 |
| URL: | https://yulab-smu.top/contribution-knowledge-mining/ |
| BugReports: | https://github.com/YuLab-SMU/wikiprofiler/issues |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-04-30 08:36:10 UTC; HUAWEI |
| Author: | Guangchuang Yu 
[aut, cre, cph],
Yihao Chen [aut] |
| Maintainer: | Guangchuang Yu <guangchuangyu@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-05-02 22:00:02 UTC |
wikiprofiler: 'WikiPathway' Based Data Integration and Visualization
Description
Queries online 'WikiPathway' graphics and allows mapping user data (e.g., expression values) on the graph. The package designs a grammar of graphic syntax that using pipe operator to add graphic layer.
Author(s)
Maintainer: Guangchuang Yu guangchuangyu@gmail.com (ORCID) [copyright holder]
Authors:
Yihao Chen olivercyh@foxmail.com
See Also
Useful links:
Report bugs at https://github.com/YuLab-SMU/wikiprofiler/issues
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
Objects exported from other packages
Description
These objects are imported from other packages. Follow the links below to see their documentation.
- ggplot2
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
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)