Reformat README

README.Rmd

@@ -54,47 +54,51 @@ 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()
+    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}
-m <- module("M00013")
-g <- pathway("ko00640") |> mutate(mod=highlight_set_nodes(m@reaction_components,how="all"))
-gg <- 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()
-gg
+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`.
@@ -105,27 +109,28 @@ 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$type == "gene"),
-                 size=2.5,
-                 color="black")+
-  with_outer_glow(geom_node_text(aes(label=converted_name,
-                                     filter=converted_name=="PCNA"),
-                                 size=2.5, color="red"),
-                  colour="white",
-                  expand=4)+
-  scale_edge_color_manual(values=viridis::plasma(11))+
-  scale_fill_viridis(name="LFC")+
-  theme_void()
+    convert_org = c("pathway","hsa","ko"),
+    numeric_attribute = pseudo_lfc)+
+    geom_edge_parallel2(
+        aes(color=subtype_name),
+        arrow = arrow(length = unit(1, 'mm')), 
+        start_cap = square(1, 'cm'),
+        end_cap = square(1.5, 'cm')) + 
+    geom_node_rect(aes(filter=.data$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()
 ```

README.md

@@ -21,6 +21,7 @@ Using `BiocManager`:
 ``` r
 BiocManager::install("ggkegg")
 ```
+
 Using `devtools`:
 
 ``` r
@@ -37,53 +38,57 @@ 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()
+    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()
 ```
 
-<img src="man/figures/README-unnamed-chunk-2-1.png" width="2400" style="display: block; margin: auto;" />
+<img src="man/figures/README-unnamed-chunk-3-1.png" width="2400" style="display: block; margin: auto;" />
 
 You can use your favorite geoms to annotate raw KEGG map combining the
 functions.
 
 ``` r
-m <- module("M00013")
-g <- pathway("ko00640") |> mutate(mod=highlight_set_nodes(m@reaction_components,how="all"))
-gg <- 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()
-gg
+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()
 ```
 
-<img src="man/figures/README-unnamed-chunk-3-1.png" width="2400" style="display: block; margin: auto;" />
+<img src="man/figures/README-unnamed-chunk-4-1.png" width="2400" style="display: block; margin: auto;" />
 
 Or customize graphics based on `ggraph`.
 
@@ -93,29 +98,30 @@ 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$type == "gene"),
-                 size=2.5,
-                 color="black")+
-  with_outer_glow(geom_node_text(aes(label=converted_name,
-                                     filter=converted_name=="PCNA"),
-                                 size=2.5, color="red"),
-                  colour="white",
-                  expand=4)+
-  scale_edge_color_manual(values=viridis::plasma(11))+
-  scale_fill_viridis(name="LFC")+
-  theme_void()
+    convert_org = c("pathway","hsa","ko"),
+    numeric_attribute = pseudo_lfc)+
+    geom_edge_parallel2(
+        aes(color=subtype_name),
+        arrow = arrow(length = unit(1, 'mm')), 
+        start_cap = square(1, 'cm'),
+        end_cap = square(1.5, 'cm')) + 
+    geom_node_rect(aes(filter=.data$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()
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png" width="3600" style="display: block; margin: auto;" />
+<img src="man/figures/README-unnamed-chunk-5-1.png" width="3600" style="display: block; margin: auto;" />