DATASET_EXTERNALSHAPE

Weiyue Liu1, Zhongyi Hua2, Tong Zhou3

Last compiled on 10 December, 2024

Introduction

The function of template DATASET_EXTERNALSHAPE is to add shape plots outside nodes. Each leaf node could have multiple items in its shape plots and the size of each item represents its associated numeric values. Highest value in the dataset have the largest size, and others are scaled down proportionally. The DATASET_EXTERNALSHAPE template belongs to the “Basic graphics” class (refer to the Class for detail information).

Typically, users draw a shape plot by entering node names, either leaf node or internal node, and their corresponding data values. Without itol.toolkit, users would have to prepare data and visualize it separately. In contrast, itol.toolkit provides a coherent workflow, allowing users to prepare data and output template file seamlessly.

Draw shape plot

This section provides an example of a shape plot through multi-column data using dataset 1 (refer to the Dataset for detail information) document for detailed information).

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

library(itol.toolkit)
library(data.table)
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)

Next, we process the metadata by replacing the missing values (representing that the template was not used in this study) with 0. By processing the data, we ended up with a data frame with the first column being the tip name and the subsequent columns being the usage frequency of the template in the study. Finally, we take the obtained data as input and visualize it using the DATASET_EXTERNALSHAPE template.

df_frequence[is.na(df_frequence)] <- 0
unit_33 <- create_unit(data = df_frequence,
                      key = "E033_external_shape_1",
                      type = "DATASET_EXTERNALSHAPE",
                      tree = tree)

It is worth noting that when using DATASET_EXTERNALSHAPE template in itol.toolkit < v1.1.1, you may encounter the problem Error in get_color(field_length, set = color) : object ‘field_length’ not found, please update itol.toolkit in this case.

Style modification

The user can adjust the shape with unit@specific_themes$externalshape$type and the shape code is shown below:
|id|shape| |—|—| |1|square| |2|circle| |3|star| |4|right triangle| |5|left triangle | For example, we can adjust the shape of unit_27 to the circle by:

unit_33@specific_themes$externalshape$type <- 2

  1. IOCAS, ↩︎

  2. CACMS, ↩︎

  3. IOCAS, ↩︎