Adjust ylim to display a complete plot

[feiyis1]

What happened?

ylim is not allowing to display the complete density distribution plot (in Extrarenal Lupus Data Mart UAT app).

sessionInfo()

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

Relevant log output

No response

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[feiyis1]

Failed to assign the issue to myself and to the "NEST Program Roadmap" project after applying for Insights Engineering User Onboarding and joining in NEST users group.

[npaszty]

@m7pr

is this something that can be sorted out easily. don't think scientists would want to present a plot that is not fully displayed.

added priority label to keep it highlighted until I hear from you about the magnitude of effort ot fix.

[m7pr]

Hey @feiyis1 and @npaszty thank you for reporting that and sorry for the late reply.

The outcome of g_density_distribution_plot() is regular ggplot so you can do whathever suits you with the output. Please see below example

#### Data preparations
library(goshawk)
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")

ADLB <- rADLB
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))
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]


#### Plot creation
g_density_distribution_plot(
  label = "Density Distribution Plot",
  data = ADLB,
  param_var = "PARAMCD",
  param = c("CRP"),
  xaxis_var = "AVAL",
  unit = "AVALU",
  color_manual = color_manual,
  color_comb = "#39ff14",
  comb_line = FALSE,
  facet_var = "AVISITCD",
  facet_ncol = 2
) -> plot
plot

The above ylim is set to c(0, 0.5) and you can scale it with ggplot2::coord_cartesian https://ggplot2.tidyverse.org/reference/coord_cartesian.html

plot + ggplot2::coord_cartesian(ylim = c(0, 2))

You can always extend ylim axis in another way, directly in the plot settings with a trick - there is a parameter hline_arb = that adds a horizontal line, which also extends ylim axis

g_density_distribution_plot(
  label = "Density Distribution Plot",
  data = ADLB,
  param_var = "PARAMCD",
  param = c("CRP"),
  xaxis_var = "AVAL",
  unit = "AVALU",
  color_manual = color_manual,
  color_comb = "#39ff14",
  comb_line = FALSE,
  hline_arb = 1.75,
  facet_var = "AVISITCD",
  facet_ncol = 2
)

But this adds a red line and an extra legend, so I would advice to call below to remove the legend and minimize the visibility of the line (hline_arb_color, hline_arb_label) ggplot2::guides(color = "none")

g_density_distribution_plot(
  label = "Density Distribution Plot",
  data = ADLB,
  param_var = "PARAMCD",
  param = c("CRP"),
  xaxis_var = "AVAL",
  unit = "AVALU",
  color_manual = color_manual,
  color_comb = "#39ff14",
  comb_line = FALSE,
  hline_arb = 1.75,
  hline_arb_color = "grey",
  hline_arb_label = "",
  facet_var = "AVISITCD",
  facet_ncol = 2
) + ggplot2::guides(color = "none")

[m7pr]

When it comes to working with this plot in a teal app with tm_g_gh_density_distribution_plot you can always use Y-Axis Range Zoom from Plot Aesthetic Settings panel.

Click Toggle to be able to provide your own limits

The code for the testing app that I used

# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  
  # original ARM value = dose value
  arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  ADSL <- rADSL
  ADLB <- rADLB
  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", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD)
    )
  
  attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
})

datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_density_distribution_plot(
      label = "Density Distribution Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      color_comb = "#39ff14",
      comb_line = TRUE,
      plot_height = c(500, 200, 2000),
      font_size = c(12, 8, 20),
      line_size = c(1, .25, 3),
      hline_arb = c(.02, .05),
      hline_arb_color = c("red", "black"),
      hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

[donyunardi]

@m7pr

I dug deeper into the issue and found the root cause.

The problem is in teal.goshawk, specifically in the code generating the Y-Axis Range Zoom slider.

This slider is generated using all visits in the data when calculating density and is applied directly to the plot as the ylim argument as the module is loaded:
https://github.com/insightsengineering/teal.goshawk/blob/edfdbba63c1460e2e225cb927bca981c44546d6b/R/tm_g_gh_density_distribution_plot.R#L333

However, the density values differ when calculated for all visits versus specific visits.

For example, this is the max density when calculated with all visits:

And here is the max density value for specific visit, i.e. Baseline:

The Baseline max density is much higher than the value used to generate the slider's max value.
This is what causing the curve to be cut off for some visits.

One possible solution is to group the analysis by visits, determine the maximum density value for each group, and then apply the highest value to the Y-Axis Range Zoom slider's max value.

The function to generate the min and max of the slider for the density is here:
https://github.com/insightsengineering/teal.goshawk/blob/edfdbba63c1460e2e225cb927bca981c44546d6b/R/utils-keep_range_slider_updated.r#L27-L30

Code to play around if needed

library(dplyr)
library(goshawk)
library(shiny)
library(teal.code)
library(teal.data)
library(teal.slice)
library(teal)
library(teal.transform)
library(teal.goshawk)

library(dplyr)
arm_mapping <- list(`A: Drug X` = "150mg QD", `B: Placebo` = "Placebo", `C: Combination` = "Combination")
ADSL <- goshawk::rADSL
ADLB <- goshawk::rADLB
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>% dplyr::mutate(AVISITCD = dplyr::case_when(AVISIT == "SCREENING" ~ "SCR", AVISIT == "BASELINE" ~ "BL", grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")), TRUE ~ as.character(NA)), AVISITCDN = dplyr::case_when(AVISITCD == "SCR" ~ -2, AVISITCD == "BL" ~ 0, grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)), TRUE ~ as.numeric(NA)), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = dplyr::case_when(ARMCD == "ARM C" ~ 1, ARMCD == 
    "ARM B" ~ 2, ARMCD == "ARM A" ~ 3), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD))
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]

stopifnot(rlang::hash(ADSL) == "843e317c3d4aeb88062cd39a9c62fe8a")
stopifnot(rlang::hash(ADLB) == "806dd83c79701cfc734f61ea83f8555e")

ADLB <- dplyr::inner_join(x = ADLB, y = ADSL[, c("STUDYID", "USUBJID"), drop = FALSE], by = c("STUDYID", "USUBJID"))

ANL <- ADLB
ANL <- ADLB %>% dplyr::filter(PARAMCD == "IGA")
p <- goshawk::g_density_distribution_plot(data = ANL, param_var = "PARAMCD", param = "IGA", xaxis_var = "PCHG", trt_group = "ARM", xlim = c(-17, 19), ylim = c(0, 0.24764), color_manual = c(`150mg QD` = "#000000", Placebo = "#3498DB", Combination = "#E74C3C"), color_comb = "#39ff14", font_size = 12, line_size = 1, facet_ncol = 2, comb_line = TRUE, hline_arb = c(0.02, 0.05), hline_arb_label = c("Horizontal Line A", "Horizontal Line B"), hline_arb_color = c("red", "black"), rug_plot = FALSE)
tbl <- goshawk::t_summarytable(data = ANL, trt_group = "ARM", param_var = "PARAMCD", param = "IGA", xaxis_var = "PCHG", font_size = 12)

[donyunardi]

Acceptance Criteria

• Graph lines should show appropriately when app is loaded for density distribution plot
• When app loaded, the max value of Y-Axis Range Zoom slider should be to maximum density value when data is subsetted by AVISITCD

[m7pr]

Confirming that the error still occurs and that I was able to reproduce with

Set filters to: ADSL -> SEX -> Male, ADSL -> AGE -> 32,36

pkgload::load_all("/teal.widgets")
pkgload::load_all("/teal")
pkgload::load_all("/teal.goshawk")

data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  
  # original ARM value = dose value
  arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  ADSL <- rADSL
  ADLB <- rADLB
  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", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD)
    )
  
  attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
})

datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_density_distribution_plot(
      label = "Density Distribution Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      color_comb = "#39ff14",
      comb_line = TRUE,
      plot_height = c(500, 200, 2000),
      font_size = c(12, 8, 20),
      line_size = c(1, .25, 3),
      hline_arb = c(.02, .05),
      hline_arb_color = c("red", "black"),
      hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

[m7pr]

Created a PR that solved the issue insightsengineering/teal.goshawk#308

[m7pr]

Fixed here insightsengineering/teal.goshawk#308