arbitrary horizontal lines to tm_g_gh_spaghettiplot #41

denisovan31415 · 2021-09-09T11:23:39Z

closes #39

to test:

library(dplyr)
library(scda)
devtools::load_all()

# original ARM value = dose value
arm_mapping <- list("A: Drug X" = "150mg QD",
                    "B: Placebo" = "Placebo",
                    "C: Combination" = "Combination")

ADSL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
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", stringr::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),
    hline_1 = 78,
    hline_2 = 50)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], 'label') <- var_labels[["ACTARM"]]

app <- teal::init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset(
      "ADLB",
      ADLB,
      code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb
              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', stringr::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),
                  hline_1 = 78,
                  hline_2 = 50)
               attr(ADLB[['ARM']], 'label') <- var_labels[['ARM']]
               attr(ADLB[['ACTARM']], 'label') <- var_labels[['ACTARM']]",
      vars = list(arm_mapping = arm_mapping)),
    check = TRUE
    ),
  modules = root_modules(
    tm_g_gh_spaghettiplot(
      label = "Spaghetti Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      idvar = "USUBJID",
      xaxis_var = choices_selected(c("Analysis Visit Code" = "AVISITCD"), "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL","CHG", "PCHG"), "AVAL"),
      filter_var = choices_selected(c("None" = "NONE", "Screening" = "BASE2", "Baseline" = "BASE"),
       "NONE"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_comb = "#39ff14",
      man_color = c('Combination' = "#000000",
                   'Placebo' = "#fce300",
                   '150mg QD' = "#5a2f5f"),
      hline_vars = c("hline_1", "hline_2"),
      hline_vars_colors = c("pink", "yellow"),
      hline_vars_labels = c("Top", "Bottom")
    )
  )
)

shinyApp(app$ui, app$server)

npaszty · 2021-09-09T14:35:32Z

@junlueZH
this looks great!

The pull down for the horizontal lines is going to be populated by the ANRLO, ANRHI, LLOQN and ULOQN variables. These variables all have labels and those labels would be used for the legend labels.
In the example you are passing labels via the hline_var_labels argument which wouldn't be needed if this functionality was purely driven by the variable labels. I tested this by adding labels to the two variables and commenting out the label argument and that worked too. 👍

So the only remaining item is to bring the arbitrary hline out of the plot aesthetic section and label these updated UIs per the mock I provided in issue #2

good progress, I think we're almost there.

denisovan31415 · 2021-09-09T15:18:03Z

@npaszty

implemented:

npaszty · 2021-09-09T18:26:32Z

@junlueZH
need a free text field that would be the label for the arbitrary line. the three goshawk arguments for the arbitrary horizontal line are the following so the label has to come from the UI.
hline_arb = NULL,
hline_arb_color = "red",
hline_arb_label = NULL,

please refer to the mockup in issue #2

denisovan31415 · 2021-09-09T20:29:09Z

@npaszty

kpagacz · 2021-09-10T06:22:07Z

What is "spaigeitti"?

R/tm_g_gh_spaghettiplot.R

gogonzo

LGTM - I leave this PR to @npaszty supervision

npaszty · 2021-09-10T16:13:23Z

@junlueZH
not I see the arbitrary line label UI but when I add text it does not update the legend.

I don't see the update to the teal module function arguments that include the arguments associated with the arbitrary line.
At this point it would be much easier for testing if the roxygen example was updated so that when I pull and build we're working off data and examples and functions within the module code itself.

denisovan31415 · 2021-09-10T16:29:30Z

@npaszty

Is this what you are seeing if you run this app?

library(dplyr)
library(scda)
devtools::load_all("~/nest_projects/goshawk/")
devtools::load_all()

# original ARM value = dose value
arm_mapping <- list("A: Drug X" = "150mg QD",
                    "B: Placebo" = "Placebo",
                    "C: Combination" = "Combination")

ADSL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
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", stringr::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),
    hline_1 = 78,
    hline_2 = 50)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], 'label') <- var_labels[["ACTARM"]]

app <- teal::init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset(
      "ADLB",
      ADLB,
      code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb
              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', stringr::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),
                  hline_1 = 78,
                  hline_2 = 50)
               attr(ADLB[['ARM']], 'label') <- var_labels[['ARM']]
               attr(ADLB[['ACTARM']], 'label') <- var_labels[['ACTARM']]",
      vars = list(arm_mapping = arm_mapping)),
    check = TRUE
    ),
  modules = root_modules(
    tm_g_gh_spaghettiplot(
      label = "Spaghetti Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      idvar = "USUBJID",
      xaxis_var = choices_selected(c("Analysis Visit Code" = "AVISITCD"), "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL","CHG", "PCHG"), "AVAL"),
      filter_var = choices_selected(c("None" = "NONE", "Screening" = "BASE2", "Baseline" = "BASE"),
       "NONE"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_comb = "#39ff14",
      man_color = c('Combination' = "#000000",
                   'Placebo' = "#fce300",
                   '150mg QD' = "#5a2f5f")
      # hline_vars = c("hline1: Label for hline_1" = "hline_1", "hline2: Label for hline_2" = "hline_2"),
      # hline_vars_colors = c("pink", "yellow"),
      # hline_vars_labels = c("Top", "Bottom")
    )
  )
)

shinyApp(app$ui, app$server)

npaszty · 2021-09-10T16:37:47Z

I see the UIs associated to arbitrary line but when I type the label nothing goes into the legend. so yes on the UI and no on the update to legend.
how would this work if there is no reference to the arbitrary line arguments in the function?

denisovan31415 · 2021-09-10T19:17:52Z

@npaszty

The latest commit fixes the mean / media label not displaying

denisovan31415 · 2021-09-10T19:21:30Z

Are you referring to this range ui? still there?

npaszty · 2021-09-10T19:37:54Z

@junlueZH

seems like there are a lot of iterations and things are breaking.

now the stats line and label work
still no range UI
the arbitrary hline is broken now

are we testing against the same code?
would be helpful if you tested all the pieces together each time so that when you push an update one item isn't fixed and others broken. happy to hop on hangout to chat further.

denisovan31415 · 2021-09-10T19:43:05Z

Indeed there was a name reference bug. The latest commit fixes that:

denisovan31415 · 2021-09-10T19:52:35Z

2 regarding the range UI, can you first confirm that this is what you are referring to?:

R/tm_g_gh_spaghettiplot.R

pawelru · 2021-09-14T18:26:39Z

R/tm_g_gh_spaghettiplot.R

+  if (!is.null(hline_vars)) {
+    stopifnot(is_character_vector(hline_vars, min_length = 1))
+    if (!is.null(hline_vars_labels)) {
+      stopifnot(is_character_vector(
+        hline_vars_labels, min_length = length(hline_vars),
+        max_length = (length(hline_vars)))
+      )
+    }
+    if (!is.null(hline_vars_colors)) {
+      stopifnot(is_character_vector(
+        hline_vars_colors,
+        min_length = length(hline_vars),
+        max_length = (length(hline_vars)))
+      )
+    }
+  }
+


also, it makes sense to validate arguments in the order as they are in function definition so those should be right after validations on plot_width

implemented

added ULOQ and LLOQ values to example data added ULOQN and LLOQN variables to UI to complete the example

npaszty · 2021-09-14T21:29:20Z

@junlueZH

made some mods and pushed. things look good now for app but one issue remains with the check = TRUE value and introduction of the LLOQ and ULOQ variables in the example data.

I don't know why check = TRUE fails so changed to check = FALSE. Can you take a look for me. code looks the same between the example data and code in the app.

denisovan31415 · 2021-09-15T11:03:46Z

@npaszty

It was failing the reproducibility check because the code was generating random numbers without setting a seed.

working now:

kpagacz · 2021-09-15T11:10:47Z

Can we avoid generating random numbers in tests? If we pass a seed anyway, it doesn't really matter, we might as well use a constant.

denisovan31415 · 2021-09-15T11:28:31Z

Can we avoid generating random numbers in tests? If we pass a seed anyway, it doesn't really matter, we might as well use a constant.

implemented

@npaszty

If you wish to use the random numbers, then the last commit can be reverted.

npaszty · 2021-09-15T17:16:16Z

@junlueZH @kpagacz
the sampling was to sample records randomly within groups of PARAMCD.
what the code looks like now is that it just picks a couple of records?

the objective is to have a few records within PARAMCD that contain a "<" or ">" so that we can test and provide example to users that illustrates the LOQs. however you want to accomplish that is fine by me.

denisovan31415 · 2021-09-15T20:54:45Z

@npaszty

The final decision is up to you. Do you want to revert the last commit and use the random numbers? That could easily be done. Please let me know.

npaszty · 2021-09-15T23:05:33Z

@junlueZH @kpagacz

Something looks odd after my review.
When running the following it looks like the join is only joining the first record
ADLB %>% filter(grepl(">", LBSTRESC)) %>% with(table(PARAMCD, LBSTRESC))
LBSTRESC
PARAMCD > 73
ALT 1
CRP 0
IGA 0

The LLUQC/N and ULOQC/N values should be the same for all records of the assay. so the count should be 2800 not 1 for ALT

The example works fine and we can keep that in place though it is now different than goshawk.
is there a join that would join the one record in the ALB_LOQS to all the ALT records in the ADLB? thought left_join would do that and thought I verified in goshawk. not a show stopper but that's the intension.

This reverts commit 31099d8.

denisovan31415 · 2021-09-16T17:03:45Z

@npaszty

I have reverted the last commit to use the random numbers.

This is the output of running the line of code in your comment:

> ADLB %>% filter(grepl(">", LBSTRESC)) %>% with(table(PARAMCD, LBSTRESC))
       LBSTRESC
PARAMCD > 70 > 71 > 73
    ALT    0    0    7
    CRP    7    0    0
    IGA    0    7    0

npaszty · 2021-09-16T19:13:38Z

@junlueZH
okay then we'll go with this now as the prototype to be applied to boxplot and correlation plot.
need to update the goshawk functions to call the renamed helper functions (h_*) then the modules can be updated and I can review all this stuff.

thanks for your help.

denisovan31415 · 2021-09-16T19:55:10Z

@junlueZH
okay then we'll go with this now as the prototype to be applied to boxplot and correlation plot.
need to update the goshawk functions to call the renamed helper functions (h_*) then the modules can be updated and I can review all this stuff.

thanks for your help.

All of the goshawk functions have already been updated to call the (h_*) function. It was failing automation without the update. So I already did that before I merge your PR.

denisovan31415 added 2 commits September 9, 2021 05:40

initial fix to accommodate API change to goshawk

270f60a

new select input to spaghettiplot module for horizontal lines

cf41f4c

denisovan31415 assigned npaszty Sep 9, 2021

NEWS

148e7bc

denisovan31415 added the enhancement New feature or request label Sep 9, 2021

hline

f53799d

re labeling and moving ui

a83546d

indentation

53bf300

added arbitrary line label to legend

8c72da7

denisovan31415 changed the title ~~39 arb hori lines spaigeitti@main~~ arbitrary horizontal lines to tm_g_gh_spaghettiplot Sep 10, 2021

gogonzo self-assigned this Sep 10, 2021

gogonzo reviewed Sep 10, 2021

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Merge branch 'main' into 39_arb_hori_lines_spaigeitti@main

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gogonzo approved these changes Sep 10, 2021

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denisovan31415 added 2 commits September 10, 2021 12:57

removed unused hline parameter

b0ddb6d

fixed empty group stat lable

f7f0fe4

fixed name reference bug

0eda77e

argument reorder

beab50e

denisovan31415 commented Sep 14, 2021

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Update R/tm_g_gh_spaghettiplot.R

a5c3fe9

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denisovan31415 added 2 commits September 14, 2021 13:10

Update R/tm_g_gh_spaghettiplot.R

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docs

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pawelru reviewed Sep 14, 2021

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denisovan31415 and others added 3 commits September 14, 2021 13:43

roxygen app comment bug

b61ffb7

reorder validation code

945a6c5

updated horizontal line section labels

1f42343

added ULOQ and LLOQ values to example data added ULOQN and LLOQN variables to UI to complete the example

fixed reproducible error in roxygen app

414e4e4

docs

3f9a550

removed random numbers in roxygen app

31099d8

Revert "removed random numbers in roxygen app"

4dd7e35

This reverts commit 31099d8.

denisovan31415 merged commit eec4c68 into main Sep 16, 2021

denisovan31415 deleted the 39_arb_hori_lines_spaigeitti@main branch September 16, 2021 19:55

denisovan31415 mentioned this pull request Sep 17, 2021

Update functions to include hi/lo range and LOQs horizontal line functionality insightsengineering/goshawk#27

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arbitrary horizontal lines to tm_g_gh_spaghettiplot #41

arbitrary horizontal lines to tm_g_gh_spaghettiplot #41

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arbitrary horizontal lines to tm_g_gh_spaghettiplot #41

arbitrary horizontal lines to tm_g_gh_spaghettiplot #41

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