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insightsengineering / goshawk

Functions that plot and summarize biomarkers/labs of interest
https://insightsengineering.github.io/goshawk/
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Change automated label on `g_spaghettiplot ` #247

Closed m7pr closed 3 months ago

m7pr commented 3 months ago

This fixes issue detected in Theory app on GitLab.

image

On legend, currently we display metric phrase instead of Mean or Median. With this fix we display actual statistic name

Tested with ```r 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)) %>% mutate(ANRLO = .5, ANRHI = 1) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste("<", round(runif(1, min = .5, max = .7))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(">", round(runif(1, min = .9, max = 1.2))), 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, "LOQFL") 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 = "MEAN", hline_vars = c("ANRHI", "ANRLO"), hline_vars_colors = c("pink", "brown") ) ```
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github-actions[bot] commented 3 months ago

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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%    266-610
R/g_scatterplot.R                    130     130  0.00%    142-310
R/g_spaghettiplot.R                  101     101  0.00%    248-381
R/geom_axes_line.R                   167     167  0.00%    46-358
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: af4a33580862d9f56f4cd64e880833653ef3051a

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

m7pr commented 3 months ago

I have read the CLA Document and I hereby sign the CLA

m7pr commented 3 months ago

recheck

npaszty commented 3 months ago

@m7pr

I guess the change looks okay to me but I can only test in the study data context. so if you have done testing to ensure the label changes dynamically and you'd like to merge the update then I will update my environment and test the package from https://pharmaverse.r-universe.dev

m7pr commented 3 months ago

@npaszty I added the code that I used for testing in the main comment of this issue. We can test this function using all examples from ?goshawk::g_spaghettiplot.