christopherbarrington / helpr

tools to make r life easier

helpr

tools to make r life easier

reference

devtools::install_github('ChristopherBarrington/helpr', ref='main', dependencies=FALSE)

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helpr's Issues

new dir function

dir.create(path='scratch/fgsea_results', recursive=TRUE, showWarnings=FALSE)
system(command='rm -r scratch/fgsea_results/*')

for example

add easier way to resize but not show

software versions

eg

helpr::read_dotbabs()$Lims %>%
  sprintf(fmt='conda list -n %s --json') %>%
  system(intern=TRUE) %>%
  paste(collapse='') %>%
  fromJSON() %>%
  (function(x) sapply(x, pluck, 'name') %>% set_names(x=x)) %>%
  llply(pluck, 'version') -> project_conda_versions

archiving functions

system(command='cd scratch && zip - fgsea_results/*xlsx > ../files/fgsea_results.xlsx.zip')

for example

read msigdb file

'~/db/msigdb/h.all.v7.4.entrez.gmt' %>%
  {list(path=., ncol={count.fields(., sep='\t') %>% max()})} %>%
  {read.table(file=.$path, sep='\t', fill=TRUE, header=FALSE, col.names=c('pathway', 'url', str_c('id.', 1:.$ncol)))} %>%
  dlply(~pathway, function(x) list(url=x$url, ids=select(x, starts_with('id.')) %>% unlist(use.names=FALSE) %>% na.omit())) -> hallmark_pathways

filter dds for wald or lrt

all_dds %>%
  discard(function(x) metadata(x) %>% names() %>% is_in(x='reduced')) %>%
  names() %>%
  magrittr::extract(all_dds, .)

resizing patchworks

to build a patchwork object into a gtable:

> patchworkGrob(cplot) -> plot1

write params file function

#+ write_parameters_table_and_sbatch_parameters
parameter_sets %>% write.table(file='parameters.csv', sep=',', quote=FALSE, row.names=FALSE, col.names=FALSE)
sprintf(fmt='#SBATCH --array 1-%d:1', nrow(parameter_sets)) %>% message()
sprintf(fmt="IFS=',' read %s <<< $(head -n ${SLURM_ARRAY_TASK_ID} parameters.csv | tail -n 1)", {colnames(parameter_sets) %>% str_flatten(collapse=' ') %>% str_to_upper()}) %>% message()

make deseq2 optional

not all projects will use deseq2

clipping of y facets not working?

helpr/R/resize_panels.R

Line 103 in 0f23766

set_plot_clipping <- function(x, clip=TRUE) {