m7pr
commented
6 months ago Hi @npaszty I took some time today to investigate today and I can not reproduce this.
What version of the R packages are you using? By sessionInfo() we aimed to get an output of sessionInfo() call just after you loaded all R libraries. The output from shiny session if not that helpful as it does not contain package versions.
I tried to reproduce the issue on
- version of
goshawkinstalled from main branchremotes::install_github('insightsengineering/goshawk') - stable
goshawkversion (install.packages('goshawk', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))) - development
goshawkversion (install.packages('goshawk', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org')))
The code that I run to create the plot was taken from ?g_lineplot examples
Code
```r 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 ) ```The output that I see is dodged
Does reinstallation of the package, or resizing the plot (to have wider width) fixes the issue on your side?
npaszty
What happened?
We observed that the dodging no longer dodges while maintaining grouping around a visit tic but instead spreads the data points evenly across the plot horizontally. this makes it difficult to interpret.
The dodging by default once filters are added to produce the plot looked like this when I screen shotted last Thursday
Also hoping we could control the step value increment with a finer step resolution (.5 instead of 1 for example) to allow fine tuning, it doesn't look like that UI element is built that way. the value passed in is c(1, 0, 10) in our case which is the default position in a range from 0 to 10.
sessionInfo()
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