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ggkegg

6 Notes

6.1 Stamp function

The stamp function can be used to highlight the nodes with colored rectangles.

library(ggkegg)
ggraph(pathway("ko00270"), layout="manual", x=x, y=y)+
    geom_node_rect()+
    stamp("ko:K00789")+
    theme_minimal()

6.2 Parsing of the module definition

For module describing multiple lines of the definition (e.g. M00897), the module function tries to parse them separately. These definitions will be assigned the number (in character type).

mod <- module("M00899")


defs <- get_module_attribute(mod, "definitions")
defs[["1"]]
#> $definition_block
#> [1] "K00878"
#> 
#> $definition_kos
#> [1] "K00878"
#> 
#> $definition_num_in_block
#> [1] 1
#> 
#> $definition_ko_in_block
#> $definition_ko_in_block[[1]]
#> [1] "K00878"
defs[["2"]]
#> $definition_block
#> [1] "((K00941 K00788),K14153,K21219)"
#> 
#> $definition_kos
#> [1] "K00941" "K00788" "K14153" "K21219"
#> 
#> $definition_num_in_block
#> [1] 4
#> 
#> $definition_ko_in_block
#> $definition_ko_in_block[[1]]
#> [1] "K00941" "K00788" "K14153" "K21219"

## Extract definition 2
mod |>
  module_text("2") |> ## return data.frame
  plot_module_text() ## wrapper function

6.3 Parsing of reactions in the pathway

In the devel branch of ggkegg, the KGML of the following reactions (https://www.genome.jp/entry/R00863) in ko00270 are parsed in the below format by default.

<reaction id="237" name="rn:R00863" type="irreversible">
    <substrate id="183" name="cpd:C00606"/>
    <product id="238" name="cpd:C00041"/>
    <product id="236" name="cpd:C09306"/>
</reaction>
library(ggkegg)
reac <- pathway("ko00270")
reac |> activate(edges) |> data.frame() |> filter(reaction=="rn:R00863")
#>   from  to         type subtype_name subtype_value
#> 1   91 128 irreversible    substrate          <NA>
#> 2  128 129 irreversible      product          <NA>
#> 3  128 127 irreversible      product          <NA>
#>    reaction reaction_id pathway_id
#> 1 rn:R00863         237    ko00270
#> 2 rn:R00863         237    ko00270
#> 3 rn:R00863         237    ko00270

These edges correspond to the relationship between compound substrate or product and reaction (orthology) nodes. These edges are kept for the conversion in process_reaction, where substrate and product are directly connected by edges.

reac2 <- reac |> process_reaction()
node_df <- reac2 |> activate(nodes) |> data.frame()
reac2 |> activate(edges) |> data.frame() |>
    filter(reaction=="rn:R00863") |>
    mutate(from_name=node_df$name[from], to_name=node_df$name[to])
#>   from  to         type subtype_name subtype_value
#> 1   91 129 irreversible         <NA>          <NA>
#> 2   91 127 irreversible         <NA>          <NA>
#>    reaction reaction_id pathway_id      name bgcolor
#> 1 rn:R00863        <NA>       <NA> ko:K09758 #BFBFFF
#> 2 rn:R00863        <NA>       <NA> ko:K09758 #BFBFFF
#>   fgcolor  from_name    to_name
#> 1 #000000 cpd:C00606 cpd:C00041
#> 2 #000000 cpd:C00606 cpd:C09306

6.4 Interpolation in the raster image

The annotation_custom is used in overlay_raw_map. The interpolate option can be specified.

ggraph(pathway("hsa04110"), layout="manual", x=x, y=y) + overlay_raw_map(interpolate=TRUE) + theme_void()
ggraph(pathway("hsa04110"), layout="manual", x=x, y=y) + overlay_raw_map(interpolate=FALSE) + theme_void()