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Line Plot & Spaghetti Plot: X-Axis Label #289

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npaszty opened this issue Jul 24, 2024 · 1 comment
Closed
3 tasks done

Line Plot & Spaghetti Plot: X-Axis Label #289

npaszty opened this issue Jul 24, 2024 · 1 comment
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@m7pr
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enhancement New feature or request low-priority

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@npaszty
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npaszty commented Jul 24, 2024

Feature description

the x-axis label is AVISITCD which isn't actually correct as far as the values displayed.

because of the tick mark functionlity in this module, user can change tick label to whatever they want however it is based on AVISITCD.

the x-axis label should be changed to "Analysis Visit" instead of displaying the name of the variable as AVISITCD.

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@npaszty npaszty added enhancement New feature or request low-priority labels Jul 24, 2024
@npaszty npaszty changed the title Line Plot: X-Axis Label Line Plot & Spaghetti Plot: X-Axis Label Jul 24, 2024
@m7pr m7pr self-assigned this Jul 25, 2024
@m7pr m7pr mentioned this issue Jul 25, 2024
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This was referenced Oct 10, 2024
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m7pr added a commit to insightsengineering/goshawk that referenced this issue Oct 16, 2024
@m7pr
289 possibility to pass custom axis label for g_lineplot and `g_s…
19b2c67 
…phagettiplot` (#259)

Alternative to #250 ,
related to
insightsengineering/teal.goshawk#289

<details><summary> Code for g_lineplot </summary>

```r
# Example using ADaM structure analysis dataset.

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"]]

attr(ADLB[["AVISITCDN"]], "label") <- "CUSTOM LABEL FOR THE AXIS LABEL"
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
)

attr(ADLB[["AVISITCDN"]], "label") <- NULL
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
)

```

</details>

<details><summary>Code for `g_sphagettiplot` </summary>

```r
# Example using ADaM structure analysis dataset.

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")
attr(ADLB[["AVISITCD"]], "label") <- "CUSTOM LABEL FOR THE AXIS LABEL"

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")
)

```

</details>


# lineplot

### Custom label from attribute

<img width="460" alt="image"
src="https://github.com/user-attachments/assets/bd1e12ed-1b57-4ebf-bd0f-813e90d59fd1">

### No attribute, so take column name

<img width="455" alt="image"
src="https://github.com/user-attachments/assets/11ee8d32-2def-4063-9b37-41b6d1299c16">

# sphagettiplot

### Custom label from attribute

<img width="356" alt="image"
src="https://github.com/user-attachments/assets/b55e1ec7-e57e-41c9-badd-4dc7cb9b06d3">

### No attribute, so take column name

<img width="353" alt="image"
src="https://github.com/user-attachments/assets/f31da42f-aa09-4c60-a3bf-e624f173d1c1">
@m7pr
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m7pr commented Oct 16, 2024

Closed with insightsengineering/goshawk#259

@m7pr m7pr closed this as completed Oct 16, 2024
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289 xaxis lab for Line Plot & Spaghetti Plot insightsengineering/teal.goshawk
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@npaszty @m7pr