gt() outputs data, code & settings but no formatted table in Jupyter R notebook.

[RobertCProjects]

---

Using R package gt() example code (from https://gt.rstudio.com/) within Anaconda Jupyter notebook R (4.1.1) environment outputs lots of code but not properly formatted table. Similar issue with other example code.

#
# Note: This sample code is directly from https://gt.rstudio.com/articles/gt-datasets.html 
# 

# Get vectors of 2-letter country codes for
# each region of Oceania
Australasia <- c("AU", "NZ")
Melanesia <- c("NC", "PG", "SB", "VU")
Micronesia <- c("FM", "GU", "KI", "MH", "MP", "NR", "PW")
Polynesia <- c("PF", "WS", "TO", "TV")

# Create a gt table based on a preprocessed `countrypops`
countrypops %>%
  filter(country_code_2 %in% c(
    Australasia, Melanesia, Micronesia, Polynesia)
  ) %>%
  filter(year %in% c(1995, 2005, 2015)) %>%
  mutate(region = case_when(
    country_code_2 %in% Australasia ~ "Australasia",
    country_code_2 %in% Melanesia ~ "Melanesia",
    country_code_2 %in% Micronesia ~ "Micronesia",
    country_code_2 %in% Polynesia ~ "Polynesia",
  )) %>%
  pivot_wider(names_from = year, values_from = population) %>%
  arrange(region, desc(`2015`)) %>%
  select(-starts_with("country_code")) %>%
  gt(
    rowname_col = "country_name",
    groupname_col = "region"
  ) %>%
  tab_header(title = "Populations of Oceania's Countries in 1995, 2005, and 2015") %>%
  tab_spanner(
    label = "Total Population",
    columns = c(`1995`, `2005`, `2015`)
  ) %>%
  fmt_number(
    columns = c(`1995`, `2005`, `2015`),
    decimals = 0,
    use_seps = TRUE
  )

[exoulster]

I experienced the same issue. A quick workaround seems:

1. save the gt object in a variable
2. run gt:::as.tags.gt_tbl() to print the html table

gt_table = countrypops %>%
  gt(
    rowname_col = "country_name",
    groupname_col = "region"
  )
gt:::as.tags.gt_tbl(gt_table)

[rich-iannone]

Thanks for reporting this and sharing the screenshot as well! For sure, gt tables should detect the Jupyter notebook environment and emit HTML. I hope to get this working soon.

[bryanwhiting]

Answer above works. I do this to keep piping:

gts <- function(gt_table){
   gt:::as.tags.gt_tbl(gt_table)
}
gt(head(mtcars)) %>%
  gts()

[vishalbakshi]

Hi all, thanks for the solutions @bryanwhiting and @exoulster.

I'm running into a potentially related issue so I'm posting it here instead of opening a new issue.

When I export this R notebook in VSCode (with a gt table cell output) to PDF, instead of printing the table it prints the text Shiny tags cannot be represented in plain text (need html).

I run into this issue whether I use the built-in export to PDF:

...or run the following command from the command line:

jupyter nbconvert --to pdf "gt_table_demo.ipynb"

Setup

# data analysis imports
library(tidyverse)
library(magrittr)

# formatting tables
library(gt)

# color palettes
library(scales)

Create fake data

# create test data
data <- data.frame(
  outcome_statement = c(
    "This is a very long outcome statement which will require a wide column if it remains in one line",
    "This is a second very long outcome statement which will require a wide column if it remains in one line",
    "This is a third very long outcome statement which will require a wide column if it remains in one line"),
  value_1 = c(1000,2000,3000),
  value_2 = c(450000,300,5000),
  value_3 = c(8500, 750, 25)
)

Create formatted gt table and view it with gts function

# create gt table output
data %>%
    gt() %>% 
    tab_options(
        column_labels.font.weight = "bold",
        table.width = pct(100)
    ) %>%
    tab_style(
        style = cell_borders(
            sides = c("bottom", "right"),
            color = "#bfbfbf"
        ),
        locations = cells_body(
            columns = everything(),
            rows = everything()
        )
    ) %>%
    tab_header(
        title = "Three Values for Different Outcomes"
    ) %>%
    data_color(
        columns = c(
            value_1, 
            value_2,
            value_3),
        #colors = col_bin(colorRamp(c("#fff8eb", "#fdb734"), interpolate="spline"), domain = c(0,5005), bins = 6)
        colors = col_factor(colorRamp(c("#fff8eb", "#fdb734"), interpolate="spline"), domain = NULL)
    ) %>% 
    tab_footnote(
        footnote = "Description of Value 1",
        locations = cells_column_labels(
            columns = value_1
        )
    ) %>%
    tab_footnote(
        footnote = "Description of Value 2",
        locations = cells_column_labels(
            columns = value_2
        )
    ) %>%
    tab_footnote(
        footnote = "Description of Value 3",
        locations = cells_column_labels(
            columns = value_3
        )
    ) %>%
    cols_label(
        outcome_statement = "Outcome Statement",
        value_1 = "Value 1",
        value_2 = "Value 2",
        value_3 = "Value 3"
    ) %>%
    gts()

Output in Notebook

Output in PDF

If I don't use the gts helper function, here's the output in PDF:

[vishalbakshi]

I've found a decent workaround for now: using the weasyprint pdf-engine for pandoc:

pip install weasyprint

pandoc gt_table_demo.ipynb --pdf-engine=weasyprint -o gt_table_demo.pdf

Output PDF contains (mostly correctly) formatted gt table: