rnabioco / ggtrace Goto Github PK

• Currently all colours are included in legend when user passes a predicate to trace_position and modifies background_color
• Could update this to exclude colours that are no longer shown on the plot
• Could add a new entry to legend for the background_color, the name of this entry could be the expression passed to trace_position

to something other than black

consider eliminating glue, rlang, scales, RColorBrewer

will make for easier maintenance down the line

• Want key_glyph to show trace_color etc.

move some from README

for interactive integration with shiny

Currently an expression passed to trace_position is captured with substitute() and evaluated strictly within the context of the data. This means the user cannot use environment variables with trace_position. Ideally the user would be able to include both environment and data variables such as in the example below, which does not work with ggtrace v0.2.0.

To accomplish this, need to include a data mask (with rlang::eval_tidy()) when evaluating trace_position

create_trace_plot <- function(data, traceVar = "xVar", traceThreshold = -1) {

  pl <- ggplot(data = data, aes(xVar, yVar, fill = fill_var), color = "#000000") +
    geom_point_trace(
      trace_position = !!sym(traceVar) < traceThreshold,

      fill = "#FFFFFF",
      background_params = list(color = "#000000", fill = "#CC0000")
    ) +
    ggtitle(str_c("Threshold: ", traceThreshold))

  pl
}

• dependencies from ggplot2 documentation causing checks to fail

write tests

• remove filter and mutate
• Better way to implement?

This should result in line break:

stocks %>%
  ggplot(aes(day, value, color = name)) +
  geom_line_trace(trace_position = day < 100 | day > 1200)

To fix can add NAs instead of filtering data

• Current default fill color is white, maybe change this to black
• If predicate is passed to trace_position, will result in white points that are not outlined

• When a predicate is passed to geom_line_trace() trace_position, default ordering is changed
• Due to how line breaks are handled with trace_position predicate

# good ordering
stocks %>%
  ggplot(aes(day, value, color = name)) +
  geom_line_trace()

# bad ordering
stocks %>%
  ggplot(aes(day, value, color = name)) +
  geom_line_trace(trace_position = day < 100)

• Documentation for scale_manual functions not getting pulled from ggplot2

I don't have access to repo settings

Should we be using ggproto etc to add this layer?

https://ggplot2.tidyverse.org/articles/extending-ggplot2.html

Examples:

https://github.com/const-ae/ggsignif/blob/master/R/geom_signif.R
https://github.com/slowkow/ggrepel/blob/master/R/geom-label-repel.R

• Update ggplot2 extensions gallery to indicate the package is on CRAN

Eliminate tidyverse and cowplot because they're not in Import / Suggests

just use

library(ggplot2)
library(ggtrace)

and e.g. theme_minimal() instead of the cowplot one.

• Allow user to change background point color when passing predicate to outline_position
• Would allow used to 'fade' the unselected points to draw further contrast

First release:

• usethis::use_cran_comments()
• Update (aspirational) install instructions in README
• Proofread Title: and Description:
• Check that all exported functions have @return and @examples
• Check that Authors@R: includes a copyright holder (role 'cph')
• Check licensing of included files
• Review https://github.com/DavisVaughan/extrachecks
• merge #53

Prepare for release:

• git pull
• Check if any deprecation processes should be advanced, as described in Gradual deprecation
• devtools::build_readme()
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• rhub::check_for_cran()
• git push
• Draft blog post

Submit to CRAN:

• usethis::use_version('minor')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• git push
• usethis::use_github_release()
• usethis::use_dev_version()
• git push
• Finish blog post
• Tweet
• Add link to blog post in pkgdown news menu

• would be simpler to use 'fill' and 'color' instead of 'color' and 'trace_color'
• would eliminate the need for new 'scale' functions

• assess performance
• likely much slower than geom_point() and geom_line() since geom_*_trace() functions draw groups separately

• Order of groups changes when scale_*_manual() is used to modify aesthetics

# Order should be alphabetical (CAC, DAX, FTSE, SMI)
clrs <- c(
  CAC  = "#E69F00",
  DAX  = "#0072B2",
  SMI  = "#56B4E9",
  FTSE = "#009E73"
)

p +
  geom_line_trace(stroke = 1) +
  scale_color_manual(values = clrs)

• geom_line() needs groups so it knows how to draw each line
• groups get set when mapping variables to aesthetics (color = variable)
• when passing a predicate to trace_position, groups set by color are overwritten since the background layer by default is not outlined (color = NA)
• this does not affect geom_point_trace() since groups are not needed to correctly draw points

# works
economics_long %>%
  ggplot(aes(date, value01, color = variable)) +
  geom_line_trace()

economics_long %>%
  ggplot(aes(date, value01, fill = variable)) +
  geom_line_trace(trace_position = variable == "pce")

# broken
economics_long %>%
  ggplot(aes(date, value01, color = variable)) +
  geom_line_trace(trace_position = variable == "pce")

The main comment from CRAN is below. To my knowledge, the package doesn't modify the global environment, the <<- operator isn't used. Hmm going to look into this more..

Please do not modifiy the .GlobalEnv. This is not allowed by the CRAN policies.

• could allow user to pass a named list of parameters to control aesthetics of background data points

• remove 'KEEP_THIS_ROW_PLEASE' from aesthetics list for geom_line_trace, etc. (https://rnabioco.github.io/ggtrace/reference/geom_path_trace.html#aesthetics)

• geom_line_trace