new argument to replace axes break points #116

denisovan31415 · 2022-03-09T04:47:17Z

closes #115

test with roxygen apps

github-actions · 2022-03-09T04:51:09Z

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/g_boxplot.R                        109     109  0.00%    154-310
R/g_correlationplot.R                130     130  0.00%    260-423
R/g_density_distribution_plot.R       84      84  0.00%    129-238
R/g_lineplot.R                       246     246  0.00%    269-583
R/g_scatterplot.R                    118     118  0.00%    142-297
R/g_spaghettiplot.R                   98      98  0.00%    202-332
R/geom_axes_line.R                   190     190  0.00%    48-459
R/t_summarytable.R                    83      83  0.00%    87-205
R/utils.R                             72      72  0.00%    21-147
TOTAL                               1130    1130  0.00%

Results for commit: 81c77b6

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

npaszty · 2022-03-09T22:41:57Z

@junlueZH

density: when replace axis is TRUE get the following warnings. not when FALSE. is this something that needs to be addressed?

replace axis functionality itself looks good though

denisovan31415 · 2022-03-10T10:50:23Z

@npaszty

I am not getting those warnings on my end when running density.

I am using local R Studio with the latest staged dependencies installed.

What environment are you running it on?

denisovan31415 · 2022-03-10T12:07:43Z

@npaszty

I just ran it on BEE with the latest staged dependencies:

gogonzo

line_axis_label breaks encapsulation of straight-lines and also uses %>% instead of + to add the geom. line_axis_label should be redesigned with respect to the current straight-lines implementation. We recently had an issue especially for limiting numbers of arguments and here another argument is introduced.

In my opinion teal.goshawk and end-users should use + scale_x_continuous(breaks = ...) to set breaks manually instead of growing goshawk functions. For some reason breaks are independent on the geoms in ggplot2.

denisovan31415 · 2022-03-11T14:04:46Z

@gogonzo I can redesign it to use the + instead of the pipe.

However, I believe that it is unavoidable to have a new argument. Because if the end user is not expected to be able to do this:

p + coord_cartesian(...)

according to @npaszty

Then we cannot expect them to know:

+ scale_x_continuous(breaks = ...)

gogonzo · 2022-03-14T07:02:43Z

I don't know if there is much to do. Straight lines should not affect axis so we shouldn't make any hacks to display additional breaks for them. None of the geoms in ggplot (as far as I know) influence the axis. Axes are independent and they should only depend on limits. This PR was problematic and I think it should be reverted.

Also, behaviour spotted by Nick Paszty isn't something new, but in the former releases we could also see insufficient number of breaks.

2021_10_13

source("https://raw.github.roche.com/NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "2021_10_13")

# spaghetti ----
library(goshawk)
library(scda)
library(stringr)

# original ARM value = dose value
arm_mapping <- list("A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination")
color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")

ASL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
  mutate(AVISITCD = case_when(
    AVISIT == "SCREENING" ~ "SCR",
    AVISIT == "BASELINE" ~ "BL",
    grepl("WEEK", AVISIT) ~
      paste(
        "W",
        trimws(
          substr(
            AVISIT,
            start = 6,
            stop = str_locate(AVISIT, "DAY") - 1
          )
        )
      ),
    TRUE ~ NA_character_
  )) %>%
  mutate(AVISITCDN = case_when(
    AVISITCD == "SCR" ~ -2,
    AVISITCD == "BL" ~ 0,
    grepl("W", AVISITCD) ~ as.numeric(gsub("\\D+", "", AVISITCD)),
    TRUE ~ NA_real_
  )) %>%
  # use ARMCD values to order treatment in visualization legend
  mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
                         ifelse(grepl("B", ARMCD), 2,
                                ifelse(grepl("A", ARMCD), 3, NA)
                         )
  )) %>%
  mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
  mutate(ARM = factor(ARM) %>%
           reorder(TRTORD)) %>%
  mutate(ANRLO = .30, ANRHI = .75) %>%
  rowwise() %>%
  group_by(PARAMCD) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                           paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
  )) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                           paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
  )) %>%
  ungroup()
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"

# add LLOQ and ULOQ variables
ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "AVISITCD",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  xtick = c("BL", "W 1", "W 4"),
  xlabel = c("Baseline", "Week 1", "Week 4"),
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_arb = 90,
  hline_vars = c("ANRHI", "ANRLO"),
  hline_vars_colors = c("pink", "brown"),
  ylim = c(10, 90)
)

2022_01_28

source("https://raw.github.roche.com/NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "2022_01_28")

# spaghetti ----
library(goshawk)
library(scda)
library(stringr)

# original ARM value = dose value
arm_mapping <- list("A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination")
color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")

ASL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
  mutate(AVISITCD = case_when(
    AVISIT == "SCREENING" ~ "SCR",
    AVISIT == "BASELINE" ~ "BL",
    grepl("WEEK", AVISIT) ~
      paste(
        "W",
        trimws(
          substr(
            AVISIT,
            start = 6,
            stop = str_locate(AVISIT, "DAY") - 1
          )
        )
      ),
    TRUE ~ NA_character_
  )) %>%
  mutate(AVISITCDN = case_when(
    AVISITCD == "SCR" ~ -2,
    AVISITCD == "BL" ~ 0,
    grepl("W", AVISITCD) ~ as.numeric(gsub("\\D+", "", AVISITCD)),
    TRUE ~ NA_real_
  )) %>%
  # use ARMCD values to order treatment in visualization legend
  mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
                         ifelse(grepl("B", ARMCD), 2,
                                ifelse(grepl("A", ARMCD), 3, NA)
                         )
  )) %>%
  mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
  mutate(ARM = factor(ARM) %>%
           reorder(TRTORD)) %>%
  mutate(ANRLO = .30, ANRHI = .75) %>%
  rowwise() %>%
  group_by(PARAMCD) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                           paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
  )) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                           paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
  )) %>%
  ungroup()
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"

# add LLOQ and ULOQ variables
ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "AVISITCD",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  xtick = c("BL", "W 1", "W 4"),
  xlabel = c("Baseline", "Week 1", "Week 4"),
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_vars = c("ANRHI", "ANRLO"),
  hline_vars_colors = c("pink", "brown"),
  hline_arb = 1.9
)

I suggest to close this PR and revert recent changes in goshawk and teal.goshawk

denisovan31415 · 2022-03-14T15:59:54Z

@npaszty closing this ticket as discussed with @gogonzo.
issue needs to be moved to backlog to be refined and discussed.

new argument

f8a045a

denisovan31415 added the enhancement New feature or request label Mar 9, 2022

denisovan31415 requested a review from npaszty March 9, 2022 04:47

styler

9395fb3

kpagacz self-assigned this Mar 11, 2022

gogonzo self-assigned this Mar 11, 2022

gogonzo requested changes Mar 11, 2022

View reviewed changes

denisovan31415 closed this Mar 14, 2022

insights-engineering-bot unassigned gogonzo Apr 5, 2022

gogonzo deleted the 115_axes_replacement_arg@main branch April 11, 2022 04:59

gogonzo self-assigned this May 2, 2022

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new argument to replace axes break points #116

new argument to replace axes break points #116

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denisovan31415 commented Mar 14, 2022

new argument to replace axes break points #116

new argument to replace axes break points #116

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