cgpu’s gists

cgpu / soft_coded_Dropbox_dir.Rmd

Last active September 19, 2018 05:24

ExecutionPC-agnostic Dropbox directory path.

	# Find os:

	```{r}
	os <- Sys.info()[[1]]
	```

	# Create OS-relevant Dropbox file path:

	```{r}
	if(os == "Windows"){

cgpu / dataframe_2_csv_2_dataframe.R

Last active December 7, 2020 20:07

Snippet for foolproof writing of dataframes into .csv files in R

	# Preview dataframe to write beforehands:
	head(my_fav_df)

	# Check dimensions of the dataframe you wish to write in a .csv file:
	dim(my_fav_df)


	# Set path of (i)output directory (ii) filename:
	savedir = "home/cgpu/favorite_dir/"
	FILE = paste0(savedir, 'favorite_filename', '.csv')

cgpu / Rproducible.Rmd

Created August 27, 2018 06:50

	# 3 relevant packages:

	## Basic,
	```{r}
	utils::sessionInfo()
	```

	## Slightly cooler, nicer output display
	## DWNL: https://github.com/r-lib/sessioninfo
	```{r}

cgpu / slice_df_on_column_values.R

Last active May 11, 2019 13:26

Select rows from a dataframe based on a list of values contained in column of choice.

	names_to_keep <- c('item1', 'item2', 'etc')
	df_sliced <- df[is.element(df$name , names_to_keep ), ]

cgpu / PAC_analysis_pipeline.py

Created September 4, 2018 05:48

Analysis pipeline for filtering of SNPs. Not DRY or fast. For archiving purposes and future revisit.

	#!/usr/bin/env python3


	# TO RUN JUST TYPE:
	# python3 snp_selection.py

	# INPUT FILES AND OPTIONS WILL BE REQUESTED AS USER INPUT


	# THE FOLLOWING PROGRAMME IS PART OF the PACtool package (https://pypi.python.org/pypi/PACtool)

cgpu / warning_error_message_colorcoding_Rmd.Rmd

Last active September 4, 2018 11:39

	# Highlighting errors, warnings, messages
	Color code what R tells you when you need to knw something about your code.

	This cool snippet found here: https://selbydavid.com/2017/06/18/rmarkdown-alerts/<br>
	Kuddos to [David](https://twitter.com/TeaStats) for sharing!

	```{r echo=FALSE}
	# Cool snippet for color coding errors

	knitr::knit_hooks$set(

cgpu / rmd_2_word_document_format.Rmd

Last active September 11, 2018 11:47

Convert from rmarkdown to word document

	# https://rmarkdown.rstudio.com/word_document_format
	```

	---
	title: "From rmd to word document"
	date: "`r Sys.Date()`"
	output:
	word_document:
	toc : TRUE #to include a table of contents in the output
	toc_depth : 3 # Depth of headers to include in table of contents

cgpu / install_pandoc_with_installr_R_pckg.R

Created September 5, 2018 12:49

Install pandoc for cool-looking rmd outputs.

	# installing/loading the package:
	if(!require(installr)) { install.packages("installr"); require(installr)} #load / install+load installr

	# Installing pandoc
	install.pandoc()

cgpu / rmd_2_word_document_arguments.Rmd

Last active September 5, 2018 12:52

Header for knitting an rmd to word_document with arguments to tune.

	---
	title: 'My very favorite title'
	date: "`r Sys.Date()`"
	output:
	word_document:
	toc : TRUE #to include a table of contents in the output
	toc_depth : 3 # Depth of headers to include in table of contents
	fig_width : # Default width (in inches) for figures
	fig_height : # Default width (in inches) for figures
	fig_caption : TRUE #to render figures with captions

cgpu / init_df_of_know_dim_soft_coded_colnames.R

Last active January 3, 2019 13:23

Initialize dataframe with NA

	# Dataframe with the aliquot IDs of the cohort's samples, 96 x 4
	aliquot_ID <- data.frame(matrix(NA, nrow = length(ofsthelse), ncol = length(LCMS_id)))
	colnames(aliquot_ID) <- LCMS_id

Christina Chatzipantsiou cgpu