ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

https://github.com/noriakis/ggkegg

Science Score: 13.0%

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CITATION.cff file
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codemeta.json file
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Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary

Keywords

ggplot2 ggraph kegg pathway r tidygraph visualization

Last synced: 6 months ago · JSON representation

Repository

Analyzing and visualizing KEGG information using the grammar of graphics

Basic Info

Host: GitHub
Owner: noriakis
License: mit
Language: R
Default Branch: main
Homepage: https://noriakis.github.io/software/ggkegg
Size: 14.8 MB

Statistics

Stars: 232
Watchers: 7
Forks: 16
Open Issues: 11
Releases: 0

Topics

ggplot2 ggraph kegg pathway r tidygraph visualization

Created almost 3 years ago · Last pushed 11 months ago

Metadata Files

Readme Changelog License

README.Rmd

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  fig.dev = "grDevices::png",
  dpi = 300L,
  dev.args = list(),
  fig.ext = "png",
  fig.height=8,
  fig.width=12,
  fig.retina = 2L,
  fig.align = "center"
)
```

# ggkegg


[![R-CMD-check](https://github.com/noriakis/ggkegg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/noriakis/ggkegg/actions/workflows/R-CMD-check.yaml)


A set of functions to analyse and plot the KEGG information using `tidygraph`, `ggraph` and `ggplot2`.

The detailed documentation is [here](https://noriakis.github.io/software/ggkegg) using `bookdown`.

## Installation

Using `BiocManager`:

```{r, eval=FALSE}
BiocManager::install("ggkegg")
```

Using `devtools`:

```{r, eval=FALSE}
devtools::install_github("noriakis/ggkegg")
```

## Examples

```{r message=FALSE, warning=FALSE, fig.width=8, fig.height=5}
library(ggkegg)
library(ggfx)
library(igraph)
library(tidygraph)
library(dplyr)

pathway("ko01100") |>
    process_line() |>
    highlight_module(module("M00021")) |>
    highlight_module(module("M00338")) |>
    ggraph(x=x, y=y) +
        geom_node_point(size=1, aes(color=I(fgcolor),
            filter=fgcolor!="none" & type!="line")) +
        geom_edge_link0(width=0.1, aes(color=I(fgcolor),
            filter=type=="line"& fgcolor!="none")) +
        with_outer_glow(
            geom_edge_link0(width=1,
                aes(color=I(fgcolor),
                    filter=(M00021 | M00338))),
            colour="red", expand=5
        ) +
        with_outer_glow(
            geom_node_point(size=1.5,
                aes(color=I(fgcolor),
                    filter=(M00021 | M00338))),
            colour="red", expand=5
        ) +
        geom_node_text(size=2,
            aes(x=x, y=y,
                label=graphics_name,
                filter=name=="path:ko00270"),
            repel=TRUE, family="sans", bg.colour="white") +
        theme_void()
```

You can use your favorite geoms to annotate raw KEGG map combining the functions.

```{r, message=FALSE, warning=FALSE, fig.width=8, fig.height=5}
compounds <- c("cpd:C00100", "cpd:C00894", "cpd:C00894", "cpd:C05668",
    "cpd:C05668", "cpd:C01013", "cpd:C01013", "cpd:C00222",
    "cpd:C00222", "cpd:C00024")
g <- pathway("ko00640") |> mutate(mod=highlight_set_nodes(compounds, how="all"))
ggraph(g, layout="manual", x=x, y=y)+
    geom_node_rect(fill="grey",aes(filter=type == "ortholog"))+
    overlay_raw_map("ko00640")+
    geom_node_point(aes(filter=type == "compound"),
        shape=21, fill="blue", color="black", size=2)+
    ggfx::with_outer_glow(
        geom_node_point(aes(filter=mod, x=x, y=y), color="red",size=2),
        colour="yellow",expand=5
    )+
    theme_void()
```

Or customize graphics based on `ggraph`.

```{r, message=FALSE, warning=FALSE}
g <- pathway("hsa04110")
pseudo_lfc <- sample(seq(0,3,0.1), length(V(g)), replace=TRUE)
names(pseudo_lfc) <- V(g)$name

ggkegg("hsa04110",
    convert_org = c("pathway","hsa","ko"),
    numeric_attribute = pseudo_lfc)+
    geom_edge_parallel2(
        aes(color=subtype_name),
        arrow = arrow(length = unit(1, 'mm')), 
        start_cap = square(1, 'cm'),
        end_cap = square(1.5, 'cm')) + 
    geom_node_rect(aes(filter=.data$type == "group"),
        fill="transparent", color="red") +
    geom_node_rect(aes(fill=numeric_attribute,
        filter=.data$type == "gene")) +
    geom_node_text(aes(label=converted_name,
        filter=.data$type == "gene"),
        size=2.5,
        color="black") +
    with_outer_glow(
        geom_node_text(aes(label=converted_name,
            filter=converted_name=="PCNA"),
            size=2.5, color="red"),
        colour="white", expand=4
    ) +
    scale_edge_color_manual(values=viridis::plasma(11)) +
    scale_fill_viridis(name="LFC") +
    theme_void()
```

Owner

Login: noriakis
Kind: user
Location: Japan

Repositories: 2
Profile: https://github.com/noriakis

GitHub Events

Total

Issues event: 13
Watch event: 21
Issue comment event: 13
Push event: 6
Fork event: 1

Last Year

Issues event: 13
Watch event: 21
Issue comment event: 13
Push event: 6
Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 44
Total pull requests: 0
Average time to close issues: 28 days
Average time to close pull requests: N/A
Total issue authors: 26
Total pull request authors: 0
Average comments per issue: 2.45
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 9
Pull requests: 0
Average time to close issues: 7 days
Average time to close pull requests: N/A
Issue authors: 7
Pull request authors: 0
Average comments per issue: 1.67
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

Ramirj (9)
noriakis (5)
wangshiming (3)
TimothyStephens (2)
hanguojun007 (2)
sunliangxing (2)
w2felix (2)
joe-jhou2 (1)
BioLaoXu (1)
ucabuk (1)
SZhengP (1)
WANGchuang715 (1)
ag1805x (1)
jijitoutou (1)
ccgallen (1)

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Packages

Total packages: 1
Total downloads:
- bioconductor 15,741 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 14
Total maintainers: 1

bioconductor.org: ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

Homepage: https://github.com/noriakis/ggkegg
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ggkegg/inst/doc/ggkegg.pdf
License: MIT + file LICENSE
Latest release: 1.6.0
published 10 months ago

Versions: 14
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 15,741 Total

Rankings

Dependent repos count: 0.0%

Stargazers count: 8.5%

Forks count: 17.6%

Average: 30.9%

Dependent packages count: 31.7%

Downloads: 96.7%

Maintainers (1)

nori@hgc.jp

Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

R >= 4.2.0 depends
XML * depends
ggplot2 * depends
ggraph * depends
igraph * depends
tidygraph * depends
AnnotationDbi * imports
BiocFileCache * imports
GetoptLong * imports
data.table * imports
dplyr * imports
grDevices * imports
magick * imports
methods * imports
org.Hs.eg.db * imports
patchwork * imports
shadowtext * imports
stats * imports
stringr * imports
tibble * imports
utils * imports
BiocStyle * suggests
bnlearn * suggests
clusterProfiler * suggests
knitr * suggests
rmarkdown * suggests

ecosyste.ms

Data

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Open Source Science

ggkegg

Science Score: 13.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

bioconductor.org: ggkegg

Rankings

Maintainers (1)

Dependencies