Skip to content

Commit

Permalink
update again
Browse files Browse the repository at this point in the history
  • Loading branch information
cvanvelt committed Feb 6, 2024
1 parent 708d47e commit cc7fb16
Show file tree
Hide file tree
Showing 3 changed files with 63 additions and 1 deletion.
62 changes: 62 additions & 0 deletions HierTree.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,68 @@ class.cols <- read_sheet(ss, sheet="classes")
```
A hierarchic structure is basically a set of nodes, with edges linking nodes. Let's create an edge list for plotting using the <igraph> package.

```{r, echo=F, eval=F}
#' Create hierarchical data frame for hierarchical visualization
#'
#' @author Cindy van Velthoven
#'
#' @param cl.df level annotations
#' @param levels hierarchical levels to be visualized
#' @param rootname the name to be given to the center of the plot. Default is "total"
#'
#'
#' @usage hierDF <- as.hierDF(cl.df, levels = c("class_id_label", "subclass_id_label","supertype_id_label"),rootname="wmb")
#'
#' @return Dataframe with hierarchical representation of
as.hierDF <- function(cl.df,
levels=c("class_id_label","subclass_id_label","supertype_id_label"),
rootname="all") {
sub.df <- cl.df[,levels]
## set root (center)
sub.df <- data.frame(root = rootname, sub.df)
## add the first label set == all labels == root
hierarchyList <- list()
hierDF <- data.frame(parent = character(),
child = character())
for(i in seq_along(levels)){
print(i)
currentCols <- c("root", levels)
parentCols <- currentCols[i]
idCols <- currentCols[(i+1)]
if(is.numeric(sub.df[[idCols]])){
sub.df[[idCols]] <- as.character(as.numeric(sub.df[[idCols]]))
maxchar <- max(nchar(sub.df[[idCols]]))
sub.df[[idCols]] <- stringr::str_pad(sub.df[[idCols]] ,maxchar, pad = "0")
}
currentDF <- sub.df %>%
group_by(.data[[parentCols]],
.data[[idCols]]) %>%
summarise(values=n()) %>%
select(.data[[parentCols]],
.data[[idCols]])
colnames(currentDF) <- c("parent","child")
hierDF <- rbind(hierDF,currentDF)
}
return(hierDF)
}
```


```{r create tree, fig.width=12, fig.height=4, echo=T}
source("R/as.hierDF.R")
Expand Down
2 changes: 1 addition & 1 deletion docs/HierTree.html
Original file line number Diff line number Diff line change
Expand Up @@ -486,7 +486,7 @@ <h2>Plotting a hierarchical tree</h2>
<p><img src="HierTree_files/figure-html/plot%20tree-1.png" width="1152" /></p>
</div>

<div id="rmd-source-code">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</div>
<div id="rmd-source-code">---
title: "HierTree"
output:
  html_document:
    toc: true
    toc_float: true
    code_download: true
    code_folding: show
date: "2024-02-06"
---

## Plotting a hierarchical tree

This script can be used to plot a hierarchical tree like the one presented in Yao et al., 2023 Figure 1.
The input can be a data frame with rows representing the leaf-level and columns represent annotations. This data frame needs to be restructured to a parent-child (hierarchical network data frame), which is what the 'as.hierDF' does. 

```{r klippy, echo=FALSE, include=TRUE}
klippy::klippy()
```

```{r setup, include=FALSE} 
knitr::opts_chunk$set(warning = FALSE, message = FALSE) 
```

```{r loading libs, echo=T}


library(dplyr)
library(ggplot2)
library(ggnewscale)
library(googlesheets4)
library(ggraph)
library(igraph)
library(tidyverse)
#theme_set(theme_void())
library(ggrepel)

```

Let's start by loading some dummy hierarchical data.

```{r load gsheets}
gs4_deauth()

ss <- "https://docs.google.com/spreadsheets/d/1VMs1Vs6hhNDYuUQsgBpwDiaGimPGYldR6WVS2WiS5nQ/edit?usp=sharing"
cl.df <- read_sheet(ss, sheet="cl.df")

st_colors = read_sheet(ss, sheet = "supertypes")
sub.cols <- read_sheet(ss, sheet="subclasses")
class.cols <- read_sheet(ss, sheet="classes")

```
A hierarchic structure is basically a set of nodes, with edges linking nodes. Let's create an edge list for plotting using the <igraph> package.

```{r, echo=F, eval=F}
#' Create hierarchical data frame for hierarchical visualization 
#'
#' @author Cindy van Velthoven
#'
#' @param cl.df level annotations
#' @param levels hierarchical levels to be visualized
#' @param rootname the name to be given to the center of the plot. Default is "total"
#'
#' 
#' @usage hierDF <- as.hierDF(cl.df, levels = c("class_id_label", "subclass_id_label","supertype_id_label"),rootname="wmb")
#' 
#' @return Dataframe with hierarchical representation of 

as.hierDF <- function(cl.df, 
                      levels=c("class_id_label","subclass_id_label","supertype_id_label"),
                      rootname="all") {
  
  sub.df <- cl.df[,levels]
  
  ## set root (center)
  sub.df <- data.frame(root = rootname, sub.df)
  
  
  ## add the first label set == all labels == root
  hierarchyList <- list()
  
  hierDF <- data.frame(parent = character(),
                       child = character())
  
  for(i in seq_along(levels)){
    print(i)
    
    currentCols <- c("root", levels)
    
    parentCols <- currentCols[i]
    idCols <- currentCols[(i+1)]
    
    
    if(is.numeric(sub.df[[idCols]])){
      sub.df[[idCols]] <- as.character(as.numeric(sub.df[[idCols]]))
      maxchar <- max(nchar(sub.df[[idCols]]))
      sub.df[[idCols]] <- stringr::str_pad(sub.df[[idCols]] ,maxchar, pad = "0")
    }
    
    currentDF <- sub.df %>%
      group_by(.data[[parentCols]],
               .data[[idCols]]) %>% 
      summarise(values=n()) %>%
      select(.data[[parentCols]],
             .data[[idCols]])
    
    colnames(currentDF) <- c("parent","child")
    hierDF <- rbind(hierDF,currentDF)
  }
  
  
  return(hierDF)
}
```


```{r create tree, fig.width=12, fig.height=4, echo=T}
source("R/as.hierDF.R")


hierDF <- as.hierDF(cl.df, levels = c("class_id_label", "subclass_id_label","supertype_id_label"),rootname="wmb")
# Create a graph object
graph <- graph_from_data_frame( hierDF)


dummy <- ggraph(graph, layout = 'dendrogram', circular = FALSE) + 
  geom_edge_diagonal()

dend_leaves <- dummy[["data"]] %>% filter(leaf == TRUE)

n_leaves <- nrow(dend_leaves)

dend_leaves <- dend_leaves %>% left_join(st_colors[,c("supertype_id_label", "supertype_color","supertype_id")], by=c("name"="supertype_id_label"))

subclass.df <- dummy[["data"]] %>% filter(name %in% sub.cols$subclass_id_label) %>% left_join(sub.cols[,c("subclass_id_label","subclass_id", "subclass_color")], by=c("name"="subclass_id_label"))
subclass.df$subclass_id <- gsub( " .*$", "", subclass.df$name) 

class.df <-  dummy[["data"]] %>% filter(name %in% class.cols$class_id_label) %>% left_join(class.cols[,c("class_id_label", "class_color")], by=c("name"="class_id_label"))

```
Next use ggraph to plot the 'dendrogram' and add additional layers of labeling using standard ggplot.

```{r create plot, fig.width=11, fig.height=2, eval=T, echo=T}
flat_plot = ggraph(graph, layout = 'dendrogram', circular = FALSE) + 
  geom_edge_diagonal(width = 0.25,
                     color="grey50") +
  #supertype
  geom_point(data = dend_leaves, 
             aes(x=x, y=y, color=supertype_color),
             cex=1,
             shape=19) +
  scale_color_identity(guide = "none") +
  # subclass
  new_scale_color() +
  geom_point(data=subclass.df, 
             aes(x=x, y=y, color= subclass_color),
             cex=2,
             shape=19)+
  geom_text(data=subclass.df, 
             aes(x=x, y=y, label= subclass_id),
             size=3,hjust=0, vjust=0.5,
             angle=90)+ #,             direction='y')+
    scale_color_identity(guide = "none") +
  # class
  new_scale_color() +
  geom_point(data=class.df, 
             aes(x=x, y=y, color= class_color),
             cex=2,
             shape=19)+
  geom_text_repel(data=class.df, 
             aes(x=x, y=y, label= name),
             size=3,hjust=1, vjust=0.5,
             direction='y')+
  scale_color_identity(guide = "none") +
  # add other levels if needed
  geom_text(data=dend_leaves,
            aes(x = x,
                y = y-0.1,
                label = name),
            angle = 90,
            hjust = 1.0,
            vjust = 0.5,
            size = 3,
            lineheight=0.1) +
  scale_x_continuous(limits = c(-1,n_leaves + 1),
                     expand=c(0,0)) +  
  coord_cartesian(clip = 'off')  +
  theme_void()  +
  theme(plot.margin = margin(t = 0, r = 0, b = 120, l = 0,))
  


```

```{r plot tree, fig.width=12, fig.height=4,echo=F}
flat_plot
```


</div>


</div>
Expand Down
Binary file modified docs/HierTree_files/figure-html/plot tree-1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit cc7fb16

Please sign in to comment.