Live coding gantt

gantt.R

## Load required libraries
library("googlesheets4")
library("dplyr")
library("ggplot2")
library("plotly")
## For reproducibility
library("sessioninfo")

## Authenticate with Google
googlesheets4::gs4_auth()

## Read in the data from Keri's Google Sheet
data_keri <-
    read_sheet(
        "https://docs.google.com/spreadsheets/d/1oRmRly0afPnXAxMcibWbq5G5lWI8Oz1n23jUTqLaqMk/edit#gid=0",
        sheet = "Sheet1"
    )

## Explore the data in RStudio
View(data_keri)

## Obtain the study info
studies <-
    data_keri[[1]][!complete.cases(data_keri) & !is.na(data_keri[[1]])]

## Drop the last study that has no dates
studies <- studies[-length(studies)]

## Keep only the dates
clean <- data_keri[complete.cases(data_keri), ]

## Add the stuies
clean$study <- rep(studies, each = 2)

## Simplify some column names
colnames(clean)[1] <- "stage"
colnames(clean) <- gsub(" ", "_", colnames(clean))

## Remove "Data " from the stage
clean$stage <- gsub("Data ", "", clean$stage)

## Explore in RStudio the clean data
View(clean)

## Search a bit on Google:
## https://lmgtfy.app/?q=gantt+chart+ggplot2

## Taken from https://jtr13.github.io/cc19/gantt-charts.html :
## transform to Date objects
clean <-
    mutate(clean,
        start = as.Date(Target_Start),
        end = as.Date(Target_End)
    )

## Adapted from https://plotly.com/ggplot2/gantt/ :
## make the gantt chart
p <- ggplot(clean) +
    geom_linerange(aes(
        y = study,
        xmin = Target_Start,
        xmax = Target_End,
        colour = stage
    ),
    size = I(5)
    ) +
    theme_minimal()

## View as a static plot
p

## View as an interactive plot
## Note how the "size" only affects the static plot
ggplotly(p)
## Export to html with RStudio
## https://www.biostars.org/p/458325/#458340

## Save as a pdf
pdf("gantt.pdf", width = 7, height = 3)
p
dev.off()

## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#  setting  value
#  version  R Under development (unstable) (2022-02-28 r81833)
#  os       macOS Monterey 12.2.1
#  system   aarch64, darwin20
#  ui       RStudio
#  language (EN)
#  collate  en_US.UTF-8
#  ctype    en_US.UTF-8
#  tz       America/Mexico_City
#  date     2022-03-24
#  rstudio  2021.09.2+382 Ghost Orchid (desktop)
#  pandoc   NA
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#  package       * version date (UTC) lib source
#  assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
#  brio            1.1.3   2021-11-30 [1] CRAN (R 4.2.0)
#  cachem          1.0.6   2021-08-19 [1] CRAN (R 4.2.0)
#  callr           3.7.0   2021-04-20 [1] CRAN (R 4.2.0)
#  cellranger      1.1.0   2016-07-27 [1] CRAN (R 4.2.0)
#  cli             3.2.0   2022-02-14 [1] CRAN (R 4.2.0)
#  colorout        1.2-2   2022-03-01 [1] Github (jalvesaq/colorout@79931fd)
#  colorspace      2.0-3   2022-02-21 [1] CRAN (R 4.2.0)
#  crayon          1.5.0   2022-02-14 [1] CRAN (R 4.2.0)
#  data.table      1.14.2  2021-09-27 [1] CRAN (R 4.2.0)
#  DBI             1.1.2   2021-12-20 [1] CRAN (R 4.2.0)
#  desc            1.4.1   2022-03-06 [1] CRAN (R 4.2.0)
#  devtools      * 2.4.3   2021-11-30 [1] CRAN (R 4.2.0)
#  digest          0.6.29  2021-12-01 [1] CRAN (R 4.2.0)
#  dplyr         * 1.0.8   2022-02-08 [1] CRAN (R 4.2.0)
#  ellipsis        0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
#  fansi           1.0.2   2022-01-14 [1] CRAN (R 4.2.0)
#  fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
#  fs              1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
#  gargle          1.2.0   2021-07-02 [1] CRAN (R 4.2.0)
#  generics        0.1.2   2022-01-31 [1] CRAN (R 4.2.0)
#  ggplot2       * 3.3.5   2021-06-25 [1] CRAN (R 4.2.0)
#  glue            1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
#  googledrive     2.0.0   2021-07-08 [1] CRAN (R 4.2.0)
#  googlesheets4 * 1.0.0   2021-07-21 [1] CRAN (R 4.2.0)
#  gtable          0.3.0   2019-03-25 [1] CRAN (R 4.2.0)
#  hms             1.1.1   2021-09-26 [1] CRAN (R 4.2.0)
#  htmltools       0.5.2   2021-08-25 [1] CRAN (R 4.2.0)
#  htmlwidgets     1.5.4   2021-09-08 [1] CRAN (R 4.2.0)
#  httr            1.4.2   2020-07-20 [1] CRAN (R 4.2.0)
#  jsonlite        1.8.0   2022-02-22 [1] CRAN (R 4.2.0)
#  lazyeval        0.2.2   2019-03-15 [1] CRAN (R 4.2.0)
#  lifecycle       1.0.1   2021-09-24 [1] CRAN (R 4.2.0)
#  lubridate       1.8.0   2021-10-07 [1] CRAN (R 4.2.0)
#  magrittr        2.0.2   2022-01-26 [1] CRAN (R 4.2.0)
#  memoise         2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
#  munsell         0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
#  pillar          1.7.0   2022-02-01 [1] CRAN (R 4.2.0)
#  pkgbuild        1.3.1   2021-12-20 [1] CRAN (R 4.2.0)
#  pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
#  pkgload         1.2.4   2021-11-30 [1] CRAN (R 4.2.0)
#  plotly        * 4.10.0  2021-10-09 [1] CRAN (R 4.2.0)
#  prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
#  processx        3.5.2   2021-04-30 [1] CRAN (R 4.2.0)
#  prompt          1.0.1   2022-03-01 [1] Github (gaborcsardi/prompt@7ef0f2e)
#  ps              1.6.0   2021-02-28 [1] CRAN (R 4.2.0)
#  purrr           0.3.4   2020-04-17 [1] CRAN (R 4.2.0)
#  R6              2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
#  remotes         2.4.2   2021-11-30 [1] CRAN (R 4.2.0)
#  rlang           1.0.2   2022-03-04 [1] CRAN (R 4.2.0)
#  rprojroot       2.0.2   2020-11-15 [1] CRAN (R 4.2.0)
#  rsthemes        0.3.1   2022-03-01 [1] Github (gadenbuie/rsthemes@bbe73ca)
#  rstudioapi      0.13    2020-11-12 [1] CRAN (R 4.2.0)
#  scales          1.1.1   2020-05-11 [1] CRAN (R 4.2.0)
#  sessioninfo   * 1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
#  suncalc         0.5.0   2019-04-03 [1] CRAN (R 4.2.0)
#  testthat      * 3.1.2   2022-01-20 [1] CRAN (R 4.2.0)
#  tibble          3.1.6   2021-11-07 [1] CRAN (R 4.2.0)
#  tidyr           1.2.0   2022-02-01 [1] CRAN (R 4.2.0)
#  tidyselect      1.1.2   2022-02-21 [1] CRAN (R 4.2.0)
#  usethis       * 2.1.5   2021-12-09 [1] CRAN (R 4.2.0)
#  utf8            1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
#  vctrs           0.3.8   2021-04-29 [1] CRAN (R 4.2.0)
#  viridisLite     0.4.0   2021-04-13 [1] CRAN (R 4.2.0)
#  withr           2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
#
#  [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#
# ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────


## For styling
## styler::style_file("~/Desktop/gantt.R", transformers = biocthis::bioc_style())