Leonardo Collado-Torres lcolladotor
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| --- | |
| title: "Tobi Burns" | |
| image: "tobi.jpg" | |
| links: | |
| - label: LinkedIn | |
| url: "https://linkedin.com/" | |
| - label: Twitter | |
| url: "https://twitter.com/" | |
| - label: GitHub | |
| url: "https://github.com/" |
lcolladotor
/ bad_formatted_code.R
Created
March 14, 2025 14:48
Examples of R code that is not correctly formatted
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| # Bad examples from https://style.tidyverse.org/syntax.html | |
| x[,1] | |
| x[ ,1] | |
| x[ , 1] | |
| # Bad | |
| mean (x, na.rm = TRUE) | |
| mean( x, na.rm = TRUE ) | |
| # Bad |
lcolladotor
/ Finding sugar in more general ways.R
Last active
September 18, 2024 15:47
Searching for Sugar vs Sweetener vs Salt
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| library("tidyverse") | |
| library("here") | |
| chocolate <- readRDS(here("data", "chocolate.RDS")) | |
| ## Base R solution | |
| has_sugar <- sapply( | |
| strsplit( | |
| gsub(" ", "", gsub(".*-", "", chocolate$ingredients)), | |
| ","), | |
| function(x) { any(x == "S") } |
lcolladotor
/ reading chocolate.R
Created
September 11, 2024 14:40
Output from reprex::reprex(wd = here::here())
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| library("tidyverse") | |
| library("here") | |
| chocolate <- readRDS(here("data", "chocolate.RDS")) | |
| glimpse(chocolate) | |
| options(width = 120) | |
| sessioninfo::session_info() | |
| ## After copying the above, I ran: | |
| # reprex::reprex(wd = here::here()) |
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| ## R 4.3.2 bioc 3.18 test | |
| ```R | |
| > library("recount3") | |
| > args(recount3_cache) | |
| function (cache_dir = getOption("recount3_cache", NULL)) | |
| NULL | |
| > rse_data <- recount3::create_rse_manual( | |
| + project = "SRP045225", | |
| + project_home = "data_sources/sra", |
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| library("dplyr") | |
| library("sessioninfo") | |
| tuesdata <- tidytuesdayR::tt_load("2020-01-07") | |
| rainfall <- tuesdata$rainfall | |
| rainfall_filtered <- rainfall %>% | |
| filter(city_name == "Cuernavaca") | |
| rainfall_filtered |
lcolladotor
/ migrate_hugo_shortcode_tweet.R
Last active
May 1, 2022 06:31
Code for migrating hugo tweet shortcode. Related to https://github.com/rstudio/blogdown/issues/701
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| x <- c("/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-04-19-latin-american-r-bioconductor-developers-workshop-2018.html:44:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-06-11-mindfulness.html:27:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-07-30-harrassment-diversity-in-science-and-inspiraton-from-my-grandmother.html:24:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-13-r-gene-regulatory-interaction-formulator-for-inquiring-networks.html:132:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-17-what-about-a-lawyer-like-app-as-the-mininum-help-for-defandants-in-immigration-cases.html:110:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-10-16-ashg18-tweet-summary.html:21:1", | |
| "/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-29-why-i-applied-to-join-sni-the-mexican-national-researchers-registry.html:21:1", | |
| "/Users/leocollado/Dropbox/Code/lcollado |
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| ## Load required libraries | |
| library("googlesheets4") | |
| library("dplyr") | |
| library("ggplot2") | |
| library("plotly") | |
| ## For reproducibility | |
| library("sessioninfo") | |
| ## Authenticate with Google | |
| googlesheets4::gs4_auth() |
lcolladotor
/ 01_geometric_transformation.R
Created
March 15, 2022 13:45
For https://github.com/drighelli/SpatialExperiment/issues/99. Written by @Nick-Eagles.
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| library('SpatialExperiment') | |
| library('ggplot2') | |
| library('gridExtra') | |
| library('ggspavis') | |
| id = 'V10B01-085_A1' | |
| spe_path = '/dcs04/lieber/lcolladotor/spatialHPC_LIBD4035/spatial_hpc/processed-data/pilot_data_checks/spe_basic.Rdata' | |
| ################################################################################ | |
| # Function Definitions |
lcolladotor
/ all_metrics.csv
Last active
July 23, 2021 13:57
2021-07-23 Another look at the ggpubr package https://docs.google.com/document/d/1Fai7GWsZtrIdLHBMqp_WthiJoKC45ZgYmkFJwRqRrnA/edit?usp=sharing
We can make this file beautiful and searchable if this error is corrected: It looks like row 5 should actually have 20 columns, instead of 12 in line 4.
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| "","Sample.ID","Number.of.Reads","Mean.Reads.per.Spot","Median.Genes.per.Spot","Median.UMI.Counts.per.Spot","Valid.Barcodes","Sequencing.Saturation","Q30.Bases.in.Barcode","Q30.Bases.in.RNA.Read","Q30.Bases.in.UMI","Reads.Mapped.to.Genome","Reads.Mapped.Confidently.to.Genome","Reads.Mapped.Confidently.to.Intergenic.Regions","Reads.Mapped.Confidently.to.Intronic.Regions","Reads.Mapped.Confidently.to.Exonic.Regions","Reads.Mapped.Confidently.to.Transcriptome","Reads.Mapped.Antisense.to.Gene","Total.Genes.Detected","study" | |
| "1","V10A27004_A1_Br3874",250388898,50995.7022403259,1302,2348,96.1,91.9,96.2,93.9,95.8,95.1,79.8,8.7,2.3,68.7,66.4,1,22439,"VisiumIF" | |
| "2","V10A27004_D1_Br3880",173548606,37646.1184381779,1155,2058,95.6,89.5,96.4,93.8,95.8,95.2,74.3,5.8,2.7,65.8,62.9,1.5,22355,"VisiumIF" | |
| "3","V10A27106_A1_Br3874",316562059,75605.9371865297,1347,2176,96.7,93.6,96.3,94,95.7,95,78.1,10.3,4.4,63.3,61.6,0.6,22809,"VisiumIF" | |
| "4","V10A27106_B1_Br3854",204558515,76157.3026805659,1126.5,1938,96.6,94,96.4,94.5,95.8,96.9 |
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