g_forest() clipping the output

[cicdguy]

Original message

Reporting an Issue with tern

g_forest() output is clipped when width is not large enough, when used within an RStudio session while developing code this is uncomfortable. I tried increasing par() argument without success.

Even when saving the plot in a PDF file with pdf() you need multiple trial and errors to get the width large enough for the plot to show correctly.

Is there a way to make g_forest() behave like a "normal" plot?

Here's a MRE, is simply what is in the help file of g_forest()

library(random.cdisc.data)
library(dplyr)

ADSL <- radsl(seed = 1)
ADTTE <- radtte(ADSL, seed = 2)

ADTTE_f <- ADTTE %>% 
  filter(PARAMCD == "OS" & ARMCD %in% c("ARM B", "ARM A")) %>%
  mutate(ARMCD = droplevels(ARMCD))

tbl <- t_forest_tte(
  tte = ADTTE_f$AVAL,
  is_event = ADTTE_f$CNSR == 0,
  col_by = ADTTE_f$ARMCD, 
  group_data = droplevels(ADTTE_f[, c("SEX", "RACE")]), # note factors required
  ties = "exact",
  dense_header = TRUE
)

# note plot requires a certain width
g_forest(
  tbl = tbl,
  col_x = 8,
  col_ci = 9,
  vline = 1,
  forest_header = c("Treatement\nBetter", "Comparison\nBetter"),
  xlim = c(.1, 10),
  logx = TRUE,
  x_at = c(.1, 1, 10)
)

## save graph on file
pdf(file = "test-g_forest.pdf", width = 10, height = 8)
g_forest(
  tbl = tbl,
  col_x = 8,
  col_ci = 9,
  vline = 1,
  forest_header = c("Treatement\nBetter", "Comparison\nBetter"),
  xlim = c(.1, 10),
  logx = TRUE,
  x_at = c(.1, 1, 10)
)
dev.off()

> utils::sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] teal.modules.clinical_0.6.0 teal.utils_0.0.1            random.cdisc.data_0.2.0    
 [4] tern_0.6.1                  rtables_0.1.1               teal_0.6.0                 
 [7] shiny_1.3.1                 kableExtra_1.1.0            data.table_1.12.2          
[10] magrittr_1.5                forcats_0.4.0               stringr_1.4.0              
[13] dplyr_0.8.0.1               purrr_0.3.2                 readr_1.3.1                
[16] tidyr_0.8.3                 tibble_2.1.1                tidyverse_1.2.1            
[19] rocheBCE_2.4                readxl_1.3.1                rms_5.1-3                  
[22] SparseM_1.77                Hmisc_4.2-0                 ggplot2_3.1.1              
[25] Formula_1.2-3               lattice_0.20-38             glmnet_2.0-16              
[28] foreach_1.4.4               Matrix_1.2-17               survival_2.44-1.1          
[31] DescTools_0.99.28           knitr_1.22                  ROCR_1.0-7                 
[34] gplots_3.0.1.1             

loaded via a namespace (and not attached):
 [1] nlme_3.1-139        bitops_1.0-6        lubridate_1.7.4     webshot_0.5.1      
 [5] RColorBrewer_1.1-2  httr_1.4.0          tools_3.5.3         backports_1.1.4    
 [9] R6_2.4.0            rpart_4.1-15        KernSmooth_2.23-15  lazyeval_0.2.2     
[13] colorspace_1.4-1    nnet_7.3-12         withr_2.1.2         tidyselect_0.2.5   
[17] gridExtra_2.3       compiler_3.5.3      cli_1.1.0           rvest_0.3.3        
[21] quantreg_5.38       htmlTable_1.13.1    expm_0.999-4        xml2_1.2.0         
[25] sandwich_2.5-1      caTools_1.17.1.2    scales_1.0.0        checkmate_1.9.1    
[29] polspline_1.1.14    mvtnorm_1.0-10      digest_0.6.18       foreign_0.8-71     
[33] rmarkdown_1.12      base64enc_0.1-3     pkgconfig_2.0.2     htmltools_0.3.6    
[37] manipulate_1.0.1    htmlwidgets_1.3     rlang_0.3.4         rstudioapi_0.10    
[41] generics_0.0.2      zoo_1.8-5           jsonlite_1.6        gtools_3.8.1       
[45] acepack_1.4.1       Rcpp_1.0.1          munsell_0.5.0       yaml_2.2.0         
[49] stringi_1.4.3       multcomp_1.4-10     MASS_7.3-51.3       plyr_1.8.4         
[53] gdata_2.18.0        promises_1.0.1      crayon_1.3.4        haven_2.1.0        
[57] splines_3.5.3       hms_0.4.2           pillar_1.3.1        boot_1.3-20        
[61] codetools_0.2-16    glue_1.3.1          packrat_0.5.0       evaluate_0.13      
[65] latticeExtra_0.6-28 modelr_0.1.4        httpuv_1.5.1        MatrixModels_0.4-1 
[69] cellranger_1.1.0    gtable_0.3.0        assertthat_0.2.1    xfun_0.5           
[73] mime_0.6            xtable_1.8-3        broom_0.5.2         later_0.8.0        
[77] viridisLite_0.3.0   iterators_1.0.10    cluster_2.0.8       TH.data_1.0-10    ```


Provenance: 

Creator: mattielf

## Still error

```R
library(scda)
library(tern)
library(dplyr)

adtte <- synthetic_cdisc_data("latest")$adtte

# Save variable labels before data processing steps.
adtte_labels <- formatters::var_labels(adtte)

adtte_f <- adtte %>%
  filter(
    PARAMCD == "OS",
    ARM %in% c("B: Placebo", "A: Drug X"),
    SEX %in% c("M", "F")
  ) %>%
  mutate(
    # Reorder levels of ARM to display reference arm before treatment arm.
    ARM = droplevels(forcats::fct_relevel(ARM, "B: Placebo")),
    SEX = droplevels(SEX),
    AVALU = as.character(AVALU),
    is_event = CNSR == 0
  )


df <- extract_survival_subgroups(
  variables = list(
    tte = "AVAL",
    is_event = "is_event",
    arm = "ARM", subgroups = c("SEX", "BMRKR2")
  ),
  data = adtte_f
)

table_hr <- basic_table() %>%
  tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1])

g_forest(table_hr)

Expect

Only get the following

[cicdguy]

I have made a minimum width for the table columns, hence only the "forest" part is resizing. The minimal column width might be a bit conservative, I will have a look at it.

Provenance:

Creator: waddella

[shajoezhu]

we should close this with insightsengineering/teal.modules.clinical#911 now

[edelarua]

Closed by #1158