fix g_lineplot

[gogonzo]

linking to insightsengineering/teal.goshawk#264

Table below a lineplot displays "center" and "count" instead of values - see the code and images below

pkgload::load_all("goshawk")
library(stringr)
library(dplyr)
library(nestcolor)

# original ARM value = dose value
arm_mapping <- list(
  "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination"
)
color_manual <- c("150mg QD" = "thistle", "Placebo" = "orange", "Combination" = "steelblue")
type_manual <- c("150mg QD" = "solid", "Placebo" = "dashed", "Combination" = "dotted")

ADSL <- rADSL %>% filter(!(ARM == "B: Placebo" & AGE < 40))
ADLB <- rADLB
ADLB <- right_join(ADLB, ADSL[, c("STUDYID", "USUBJID")])
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"]]

g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)

g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCD",
  color_manual = NULL,
  line_type = type_manual,
  median = TRUE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c("BL", "W 1", "W 5"),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)

g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCD",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c("BL", "W 1", "W 5"),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600,
  count_threshold = 90,
  table_font_size = 15
)

g_lineplot(
  label = "Line Plot",
  data = ADLB,
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = NULL,
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = TRUE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 600
)

g_lineplot(
  label = "Line Plot",
  data = subset(ADLB, SEX %in% c("M", "F")),
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = "SEX",
  time = "AVISITCDN",
  color_manual = color_manual,
  line_type = type_manual,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 1500
)

g_lineplot(
  label = "Line Plot",
  data = subset(ADLB, SEX %in% c("M", "F")),
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  shape = "SEX",
  time = "AVISITCDN",
  color_manual = NULL,
  median = FALSE,
  hline_arb = c(.9, 1.1, 1.2, 1.5),
  hline_arb_color = c("green", "red", "blue", "pink"),
  hline_arb_label = c("A", "B", "C", "D"),
  xtick = c(0, 1, 5),
  xlabel = c("Baseline", "Week 1", "Week 5"),
  rotate_xlab = FALSE,
  plot_height = 1500
)

main

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Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/g_boxplot.R                        116     116  0.00%    147-310
R/g_correlationplot.R                135     135  0.00%    251-419
R/g_density_distribution_plot.R       86      86  0.00%    125-236
R/g_lineplot.R                       275     275  0.00%    262-606
R/g_scatterplot.R                    130     130  0.00%    142-310
R/g_spaghettiplot.R                  101     101  0.00%    243-376
R/geom_axes_line.R                   167     167  0.00%    48-360
R/t_summarytable.R                   102     102  0.00%    87-224
R/utils.R                             70      70  0.00%    17-137
TOTAL                               1182    1182  0.00%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 3bbabb6

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[kartikeyakirar]

bug is fixed
Tested on sample app

Tested on sample code.
multiple_plots1.pdf