Update survival plots number formatting (4/N)

[rjcorb]

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[jharenza]

Nice updates, however, had a few issues.

1. Your FP pdfs in braf-fusions do not match mine when I rerun - I still see 3 or varied decimals in the plots. This is whether I run the script 03 or full module.
   UPDATE: I see those changes over here.
2. When re-running survival module script 03 alone, it throws an error:

Rscript --vanilla 03-plot-survival.R 
-- Attaching core tidyverse packages -------------------------------------------------------------------------------------------------------- tidyverse 2.0.0 --
v dplyr     1.1.4     v readr     2.1.5
v forcats   1.0.0     v stringr   1.5.1
v ggplot2   3.5.1     v tibble    3.2.1
v lubridate 1.9.3     v tidyr     1.3.1
v purrr     1.0.2     
-- Conflicts -------------------------------------------------------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
i Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: colorspace
Loading required package: ggpubr

Attaching package: 'survminer'

The following object is masked from 'package:survival':

    myeloma

Rows: 1484 Columns: 41
-- Column specification ----------------------------------------------------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (22): Kids_First_Biospecimen_ID, predicted_ancestry, Kids_First_Particip...
dbl (18): EAS_prob, AFR_prob, AMR_prob, SAS_prob, EUR_prob, PC1, PC2, PC3, P...
lgl  (1): given_ancestry

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in readRDS(con, refhook = refhook) : cannot open the connection
Calls: read_rds -> readRDS
In addition: Warning message:
In readRDS(con, refhook = refhook) :
  cannot open file '/home/rstudio/pbta-ancestry/analyses/survival/results/ATRT/logrank_ATRT_OS_predicted_ancestry.RDS': No such file or directory

However, when I run the whole module, it completes and the changes are as expected. So I suggest you rerun the full modules and commit all changes- maybe something got removed by accident.

[rjcorb]

ok, I've rerun and committed all RDS files. Let me know if that resolves the issue.

[jharenza]

confirming the survival module plots are now correct here, but once this is merged and then merged into 68, 68 will need a rerun since the plots here will have 3 decimals for braf fusions but in 68 they have two. merging 67 into 68 will put them back at 3....

[naqvia]

Code runs and plots generated!