DATASET_LINECHART

Longzhao Li1, Zhongyi Hua2, Tong Zhou3

Last compiled on 10 December, 2024

Introduction

The function of DATASET_LINECHART could draw the line chart and store corresponding X-axis coordinates and Y-axis coordinates. The DATASET_LINECHART template belongs to the “Basic graphics” class (refer to the Class for detail information).

Typically, users cannot save drawing information using iTOL, making it difficult to reproduce pictures or share them with others.

Here, itol.toolkit provides a convenient way to store X-axis and Y-axis coordinates for line charts. This section shows how to use itol.toolkit to draw the line chart and store corresponding information.

Draw line chart

This section uses dataset 1 as an example to show how to draw the line chart. (refer to the Dataset for detail information)

Load data

The first step is to load the newick format tree file tree_of_itol_templates.tree and its corresponding metadata df_frequence.

library(itol.toolkit)
library(data.table)
library(tidyr)
library(dplyr)
library(stringr)
library(ape)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
df_frequence <- system.file("extdata",
                            "templates_frequence.txt",
                             package = "itol.toolkit")
df_frequence <- fread(df_frequence)
names(df_frequence) <- c(
  "id",
  "Li,S. et al. (2022) J. Hazard. Mater.","Zheng,L. et al. (2022) Environ. Pollut.",
  "Welter,D.K. et al. (2021) mSystems",
  "Zhang,L et al. (2022) Nat. Commun.",
  "Rubbens,P. et al. (2019) mSystems",
  "Laidoudi,Y. et al. (2022) Pathogens",
  "Wang,Y. et al. (2022) Nat. Commun.",
  "Ceres,K.M. et al. (2022) Microb. Genomics",
  "Youngblut,N.D. et al. (2019) Nat. Commun.",
  "Balvín,O. et al. (2018) Sci. Rep.",
  "Prostak,S.M. et al. (2021) Curr. Biol.",
  "Dijkhuizen,L.W. et al. (2021) Front. Plant Sci.",
  "Zhang,X. et al. (2022) Microbiol. Spectr.",
  "Peris,D. et al. (2022) PLOS Genet.",
  "Denamur,E. et al. (2022) PLOS Genet.",
  "Dezordi,F.Z. et al. (2022) bioRxiv",
  "Lin,Y. et al. (2021) Microbiome",
  "Wang,Y. et al. (2022) bioRxiv",
  "Qi,Z. et al. (2022) Food Control",
  "Zhou,X. et al. (2022) Food Res. Int.",
  "Zhou,X. et al. (2022) Nat. Commun.")
names(df_frequence) <- stringr::str_remove_all(names(df_frequence),"[()]")
names(df_frequence) <- stringr::str_replace_all(names(df_frequence),",","-")

Data processing and create the unit

Convert wide data to long data. After conversion, the input data fed to DATASET_LINECHART should have three columns: tree tip id, X-axis coordinates, and Y-axis coordinates.

df_frequence_years <- df_frequence %>% 
  pivot_longer(-id) %>% 
  mutate(years = str_extract(name,"\\d{4}")) %>% 
  replace(is.na(.), 0) %>% 
  group_by(id,years) %>% 
  summarise(value = sum(value)) %>% 
  pivot_wider(names_from=years,values_from=value) %>% 
  replace(is.na(.), 0) %>% 
  pivot_longer(-id)
unit_40 <- create_unit(data = df_frequence_years,
                    key = "E040_linechart_1",
                    type = "DATASET_LINECHART",
                    tree = tree)

  1. IOCAS, ↩︎

  2. CACMS, ↩︎

  3. IOCAS, ↩︎