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If the provision + cannot be reformed, it shall be severed from this Public License + without affecting the enforceability of the remaining terms and + conditions. + + c. No term or condition of this Public License will be waived and no + failure to comply consented to unless expressly agreed to by the + Licensor. + + d. Nothing in this Public License constitutes or may be interpreted + as a limitation upon, or waiver of, any privileges and immunities + that apply to the Licensor or You, including from the legal + processes of any jurisdiction or authority. + +======================================================================= + +Creative Commons is not a party to its public +licenses. Notwithstanding, Creative Commons may elect to apply one of +its public licenses to material it publishes and in those instances +will be considered the “Licensor.” The text of the Creative Commons +public licenses is dedicated to the public domain under the CC0 Public +Domain Dedication. Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. + diff --git a/README.md b/README.md index f42fd9c..2164b68 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,24 @@ -# Readme +# EndoMT in the Athero-Express. + +*Athero-Express Team* + +Lotte Slenders, +Sander W. van der Laan, +Michal Mokry, +Dominique de Kleijn, +Gert Jan de Borst. + +**Project ID** [`EndoMT_in_AE`] + + +## Background + +Here we study endoMT in carotid plaques from the Athero-Express. + +## Study design + + + @@ -9,22 +29,16 @@ You can load this project in RStudio by opening the file called 'EndoMT_in_AE.Rp ## Project structure -File | Description | Usage ------------------- | -------------------------- | -------------- -README.md | Description of project | Human editable -EndoMT_in_AE.Rproj | Project file | Loads project -LICENSE | User permissions | Read only -.worcs | WORCS metadata YAML | Read only -prepare_data.R | Script to process raw data | Human editable -renv.lock | Reproducible R environment | Read only -File | Description | Usage ------------------- | -------------------------- | -------------- -README.md | Description of project | Human editable -EndoMT_in_AE.Rproj | Project file | Loads project -LICENSE | User permissions | Read only -.worcs | WORCS metadata YAML | Read only -prepare_data.R | Script to process raw data | Human editable -renv.lock | Reproducible R environment | Read only +File | Description | Usage +---------------------------| ----------------------------------- | -------------- +README.md | Description of project | Human editable +EndoMT_in_AE.Rproj | Project file | Loads project +LICENSE | User permissions | Read only +.worcs | WORCS metadata YAML | Read only +renv.lock | Reproducible R environment | Read only +images | image directory for project | Human editable +scripts | Scripts directory | Human editable + @@ -52,3 +66,53 @@ Please refer to the vignette on [reproducing a WORCS project]() for step by step + +# Acknowledgements + +Dr. Sander W. van der Laan is funded through grants from the Netherlands CardioVascular Research Initiative of the Netherlands Heart Foundation (CVON 2011/B019 and CVON 2017-20: Generating the best evidence-based pharmaceutical targets for atherosclerosis [GENIUS I&II]). We are thankful for the support of the ERA-CVD program ‘druggable-MI-targets’ (grant number: 01KL1802), the EU H2020 TO_AITION (grant number: 848146), and the Leducq Fondation ‘PlaqOmics’. + +Plaque samples are derived from carotid endarterectomies as part of the [Athero-Express Biobank Study](https://doi.org/10.1007/s10564-004-2304-6) which is an ongoing study in the UMC Utrecht. + +The framework was based on the [`WORCS` package](https://osf.io/zcvbs/). + + + +#### Changes log + + _Version:_ v1.0.0
+ _Last update:_ 2022-11-08
+ _Written by:_ Lotte Slenders; Sander W. van der Laan (s.w.vanderlaan-2[at]umcutrecht.nl). + + **MoSCoW To-Do List** + The things we Must, Should, Could, and Would have given the time we have. + _M_ + + _S_ + + _C_ + + _W_ + + **Changes log** + * v1.0.0 Initial version. + +-------------- + +#### Creative Commons BY-NC-ND 4.0 +##### Copyright (c) 1979-2022 Lotte Slenders | Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com. + +This is a human-readable summary of (and not a substitute for) the [license](LICENSE). +
+You are free to share, copy and redistribute the material in any medium or format. The licencor cannot revoke these freedoms as long as you follow the license terms.
 +
+Under the following terms:
+- Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
 +- NonCommercial — You may not use the material for commercial purposes.
 +- NoDerivatives — If you remix, transform, or build upon the material, you may not distribute the modified material.
 +- No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
 +
+Notices:
+You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. +No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. + + diff --git a/Scripts/colors.R b/Scripts/colors.R new file mode 100755 index 0000000..e0c7651 --- /dev/null +++ b/Scripts/colors.R @@ -0,0 +1,65 @@ +################################################################################ +# PROJECT COLORS # +################################################################################ + +### UtrechtScienceParkColoursScheme +### +### WebsitetoconvertHEXtoRGB:http://hex.colorrrs.com. +### Forsomefunctionsyoushoulddividethesenumbersby255. +### +### No. Color HEX (RGB) CHR MAF/INFO +###--------------------------------------------------------------------------------------- +### 1 yellow #FBB820 (251,184,32) => 1 or 1.0>INFO +### 2 gold #F59D10 (245,157,16) => 2 +### 3 salmon #E55738 (229,87,56) => 3 or 0.05 4 +### 5 lightpink #E35493 (227,84,147) => 5 or 0.8 6 +### 7 hardpink #CC0071 (204,0,113) => 7 +### 8 lightpurple #A8448A (168,68,138) => 8 +### 9 purple #9A3480 (154,52,128) => 9 +### 10 lavendel #8D5B9A (141,91,154) => 10 +### 11 bluepurple #705296 (112,82,150) => 11 +### 12 purpleblue #686AA9 (104,106,169) => 12 +### 13 lightpurpleblue #6173AD (97,115,173/101,120,180) => 13 +### 14 seablue #4C81BF (76,129,191) => 14 +### 15 skyblue #2F8BC9 (47,139,201) => 15 +### 16 azurblue #1290D9 (18,144,217) => 16 or 0.01 17 +### 18 greenblue #15A6C1 (21,166,193) => 18 +### 19 seaweedgreen #5EB17F (94,177,127) => 19 +### 20 yellowgreen #86B833 (134,184,51) => 20 +### 21 lightmossgreen #C5D220 (197,210,32) => 21 +### 22 mossgreen #9FC228 (159,194,40) => 22 or MAF>0.20 or 0.6 23/X +### 24 green #49A01D (73,160,29) => 24/Y +### 25 grey #595A5C (89,90,92) => 25/XY or MAF<0.01 or 0.0 26/MT +### +### ADDITIONAL COLORS +### 27 midgrey #D7D8D7 +### 28 verylightgrey #ECECEC" +### 29 white #FFFFFF +### 30 black #000000 +###---------------------------------------------------------------------------------------------- + +uithof_color = c("#FBB820","#F59D10","#E55738","#DB003F","#E35493","#D5267B", + "#CC0071","#A8448A","#9A3480","#8D5B9A","#705296","#686AA9", + "#6173AD","#4C81BF","#2F8BC9","#1290D9","#1396D8","#15A6C1", + "#5EB17F","#86B833","#C5D220","#9FC228","#78B113","#49A01D", + "#595A5C","#A2A3A4", "#D7D8D7", "#ECECEC", "#FFFFFF", "#000000") + +uithof_color_legend = c("#FBB820", "#F59D10", "#E55738", "#DB003F", "#E35493", + "#D5267B", "#CC0071", "#A8448A", "#9A3480", "#8D5B9A", + "#705296", "#686AA9", "#6173AD", "#4C81BF", "#2F8BC9", + "#1290D9", "#1396D8", "#15A6C1", "#5EB17F", "#86B833", + "#C5D220", "#9FC228", "#78B113", "#49A01D", "#595A5C", + "#A2A3A4", "#D7D8D7", "#ECECEC", "#FFFFFF", "#000000") + +#ggplot2 default color palette +gg_color_hue <- function(n) { + hues = seq(15, 375, length = n + 1) + hcl(h = hues, l = 65, c = 100)[1:n] +} + +### ---------------------------------------------------------------------------- \ No newline at end of file diff --git a/Scripts/create_worcs.R b/Scripts/create_worcs.R new file mode 100644 index 0000000..6914ef4 --- /dev/null +++ b/Scripts/create_worcs.R @@ -0,0 +1,9 @@ +worcs::worcs_project( + path = ".", # the current folder + manuscript = "none", # edit this if you want a manuscript + preregistration = "none", # edit this if you want a preregistration + add_license = "CC_BY-NC-ND_4.0", + use_renv = TRUE, + remote_repo = "git@github.com:CirculatoryHealth/EndoMT_in_AE.git", # add git repo + verbose = TRUE +) \ No newline at end of file diff --git a/Scripts/functions.R b/Scripts/functions.R new file mode 100755 index 0000000..0ad7749 --- /dev/null +++ b/Scripts/functions.R @@ -0,0 +1,550 @@ +################################################################################ +# GENERAL FUNCTIONS +################################################################################ + +# Auto installer +install.packages.auto <- function(x) { + x <- as.character(substitute(x)) + if(isTRUE(x %in% .packages(all.available = TRUE))) { + eval(parse(text = sprintf("require(\"%s\")", x))) + } else { + # Update installed packages - this may mean a full upgrade of R, which in turn + # may not be warrented. + #update.install.packages.auto(ask = FALSE) + eval(parse(text = sprintf("install.packages(\"%s\", dependencies = TRUE, repos = \"https://cloud.r-project.org/\")", x))) + } + if(isTRUE(x %in% .packages(all.available = TRUE))) { + eval(parse(text = sprintf("require(\"%s\")", x))) + } else { + if (!requireNamespace("BiocManager")) + install.packages("BiocManager") + BiocManager::install() # this would entail updating installed packages, which in turned may not be warrented + + # Code for older versions of R (<3.5.0) + # source("http://bioconductor.org/biocLite.R") + # Update installed packages - this may mean a full upgrade of R, which in turn + # may not be warrented. + # biocLite(character(), ask = FALSE) + eval(parse(text = sprintf("BiocManager::install(\"%s\")", x))) + eval(parse(text = sprintf("require(\"%s\")", x))) + } +} + + +################################################################################ +# (GENERAL) LINEAR/LOGISTIC MODELING +################################################################################ +# Function to grep data from glm()/lm() + +### CONTINUOUS TRAITS +GLM.CON <- function(fit, DATASET, x_name, y, verbose=c(TRUE,FALSE)){ + cat("Analyzing in dataset '", DATASET ,"' the association of '", x_name ,"' with '", y ,"' .\n") + if (nrow(summary(fit)$coefficients) == 1) { + output = c(DATASET, x_name, y, rep(NA,8)) + cat("Model not fitted; probably singular.\n") + }else { + cat("Collecting data.\n\n") + effectsize = summary(fit)$coefficients[2,1] + SE = summary(fit)$coefficients[2,2] + OReffect = exp(summary(fit)$coefficients[2,1]) + CI_low = exp(effectsize - 1.96 * SE) + CI_up = exp(effectsize + 1.96 * SE) + tvalue = summary(fit)$coefficients[2,3] + pvalue = summary(fit)$coefficients[2,4] + R = summary(fit)$r.squared + R.adj = summary(fit)$adj.r.squared + sample_size = nrow(model.frame(fit)) + N = study.samplesize + Perc_Miss = 100 - ((sample_size * 100)/N) + + output = c(DATASET, x_name, y, effectsize, SE, OReffect, CI_low, CI_up, tvalue, pvalue, R, R.adj, N, sample_size, Perc_Miss) + + if (verbose == TRUE) { + cat("We have collected the following and summarize it in an object:\n") + cat("Dataset...................:", DATASET, "\n") + cat("Score/Exposure/biomarker..:", x_name, "\n") + cat("Trait/outcome.............:", y, "\n") + cat("Effect size...............:", round(effectsize, 6), "\n") + cat("Standard error............:", round(SE, 6), "\n") + cat("Odds ratio (effect size)..:", round(OReffect, 3), "\n") + cat("Lower 95% CI..............:", round(CI_low, 3), "\n") + cat("Upper 95% CI..............:", round(CI_up, 3), "\n") + cat("T-value...................:", round(tvalue, 6), "\n") + cat("P-value...................:", signif(pvalue, 8), "\n") + cat("R^2.......................:", round(R, 6), "\n") + cat("Adjusted r^2..............:", round(R.adj, 6), "\n") + cat("Sample size of AE DB......:", N, "\n") + cat("Sample size of model......:", sample_size, "\n") + cat("Missing data %............:", round(Perc_Miss, 6), "\n") + } else { + cat("Collecting data in summary object.\n") + } + } + return(output) + print(output) +} + +### BINARY TRAITS +GLM.BIN <- function(fit, DATASET, x_name, y, verbose=c(TRUE,FALSE)){ + cat("Analyzing in dataset '", DATASET ,"' the association of '", x_name ,"' with '", y ,"' ...\n") + if (nrow(summary(fit)$coefficients) == 1) { + output = c(DATASET, x_name, y, rep(NA,9)) + cat("Model not fitted; probably singular.\n") + }else { + cat("Collecting data...\n") + effectsize = summary(fit)$coefficients[2,1] + SE = summary(fit)$coefficients[2,2] + OReffect = exp(summary(fit)$coefficients[2,1]) + CI_low = exp(effectsize - 1.96 * SE) + CI_up = exp(effectsize + 1.96 * SE) + zvalue = summary(fit)$coefficients[2,3] + pvalue = summary(fit)$coefficients[2,4] + dev <- fit$deviance + nullDev <- fit$null.deviance + modelN <- length(fit$fitted.values) + R.l <- 1 - dev / nullDev + R.cs <- 1 - exp(-(nullDev - dev) / modelN) + R.n <- R.cs / (1 - (exp(-nullDev/modelN))) + sample_size = nrow(model.frame(fit)) + N = study.samplesize + Perc_Miss = 100 - ((sample_size * 100)/N) + + output = c(DATASET, x_name, y, effectsize, SE, OReffect, CI_low, CI_up, zvalue, pvalue, R.l, R.cs, R.n, N, sample_size, Perc_Miss) + if (verbose == TRUE) { + cat("We have collected the following and summarize it in an object:\n") + cat("Dataset...................:", DATASET, "\n") + cat("Score/Exposure/biomarker..:", x_name, "\n") + cat("Trait/outcome.............:", y, "\n") + cat("Effect size...............:", round(effectsize, 6), "\n") + cat("Standard error............:", round(SE, 6), "\n") + cat("Odds ratio (effect size)..:", round(OReffect, 3), "\n") + cat("Lower 95% CI..............:", round(CI_low, 3), "\n") + cat("Upper 95% CI..............:", round(CI_up, 3), "\n") + cat("Z-value...................:", round(zvalue, 6), "\n") + cat("P-value...................:", signif(pvalue, 8), "\n") + cat("Hosmer and Lemeshow r^2...:", round(R.l, 6), "\n") + cat("Cox and Snell r^2.........:", round(R.cs, 6), "\n") + cat("Nagelkerke's pseudo r^2...:", round(R.n, 6), "\n") + cat("Sample size of AE DB......:", N, "\n") + cat("Sample size of model......:", sample_size, "\n") + cat("Missing data %............:", round(Perc_Miss, 6), "\n") + } else { + cat("Collecting data in summary object.\n") + } + } + return(output) + print(output) +} + + +################################################################################ +# REGIONAL ASSOCIATION PLOTTING +################################################################################ + + +# RACER singleRegionalAssocPlot +singlePlotRACER2 <- function (assoc_data, chr, build = "hg19", set = "protein_coding", + plotby, gene_plot = NULL, snp_plot = NULL, start_plot = NULL, + end_plot = NULL, label_lead = FALSE, + grey_colors = FALSE, + cred_set = FALSE, + gene_track_h = 3, gene_name_s = 2.5) { + if (missing(assoc_data)) { + stop("Please provide a data set to plot.") + } + else if (missing(chr)) { + stop("Please specify which chromosome you wish to plot.") + } + else if (missing(plotby)) { + stop("Please specify the method by which you wish to plot.") + } + else if (plotby == "gene") { + if (is.null(gene_plot)) { + stop("Please specify a gene to plot by.") + } + } + else if (plotby == "snp") { + if (is.null(snp_plot)) { + stop("Please specify a snp to plot by.") + } + } + else if (plotby == "coord") { + if (is.null(start_plot) | is.null(end_plot)) { + stop("Please specify start coordinate for plot.") + } + } + else { + message("All inputs are go.") + } + reqs = c("CHR", "POS", "LOG10P") + cols = colnames(assoc_data) + if (sum(reqs %in% cols) == 3) { + } + else { + stop("Association Data Set is missing a required column, please format your data set using formatRACER.R.") + } + reqs_2 = c("LD", "LD_BIN") + if (sum(reqs_2 %in% cols) == 2) { + } + else { + message("Association Data Set is missing LD data, the resulting plot won't have LD information, but you can add it using the ldRACER.R function.") + } + `%>%` <- magrittr::`%>%` + if (build == "hg38") { + utils::data(hg38) + chr_in = chr + colnames(hg38) = c("GENE_ID", "CHR", "TRX_START", "TRX_END", + "LENGTH", "GENE_NAME", "TYPE") + gene_sub = hg38[hg38$CHR == chr_in, ] + } + else if (build == "hg19") { + utils::data(hg19) + chr_in = chr + colnames(hg19) = c("GENE_ID", "CHR", "TRX_START", "TRX_END", + "LENGTH", "GENE_NAME", "TYPE") + gene_sub = hg19[hg19$CHR == chr_in, ] + } + if (set == "protein_coding") { + gene_sub = gene_sub[gene_sub$TYPE == "protein_coding", + ] + } + else { + gene_sub = gene_sub + } + if (sum(is.null(plotby)) == 1) { + stop("Please specify a method by which to plot.") + } + if (sum(is.null(plotby)) == 0) { + message("Plotting by...") + if ((plotby == "coord") == TRUE) { + message("coord") + start = start_plot + end = end_plot + } + else if ((plotby == "gene") == TRUE) { + message(paste("gene:", gene_plot)) + if (sum(is.null(gene_plot)) == 0) { + p = subset(gene_sub, gene_sub$GENE_NAME == gene_plot) + start = min(p$TRX_START) - 5e+05 + end = max(p$TRX_END) + 5e+05 + } + else { + message("No gene specified.") + } + } + else if ((plotby == "snp") == TRUE) { + message(paste("snp", snp_plot)) + q = assoc_data[assoc_data$RS_ID == snp_plot, ] + w = q$POS + w = as.numeric(as.character(w)) + start = w - 5e+05 + end = w + 5e+05 + } + } + gene_sub = subset(gene_sub, gene_sub$TRX_START > (start - + 50000)) + gene_sub = subset(gene_sub, gene_sub$TRX_END < (end + 50000)) + gene_sub = gene_sub[, c(3, 4, 6)] + gene_sub = reshape2::melt(gene_sub, id.vars = "GENE_NAME") + gene_sub$y_value = as.numeric(as.factor(gene_sub$GENE_NAME)) + plot_lab = subset(gene_sub, gene_sub$variable == "TRX_END") + message("Reading in association data") + in.dt <- as.data.frame(assoc_data) + in.dt$POS = as.numeric(as.character(in.dt$POS)) + in.dt$LOG10P = as.numeric(as.character(in.dt$LOG10P)) + in.dt$CHR = as.numeric(as.character(in.dt$CHR)) + in.dt = dplyr::filter(in.dt, .data$CHR == chr_in) + in.dt = dplyr::filter(in.dt, .data$POS > start) %>% dplyr::filter(.data$POS < + end) + if (label_lead == TRUE) { + message("Determining lead SNP") + lsnp_row = which(in.dt$LABEL == "LEAD") + label_data = in.dt[lsnp_row, ] + if (dim(label_data)[1] == 0) { + lsnp_row = in.dt[in.dt$LOG10P == max(in.dt$LOG10P), ] + label_data = lsnp_row[1, ] + } + } + + if (cred_set == TRUE) { + message("Collecting posterior probabilities") + ppsnp_row = which(in.dt$Posterior_Prob >= 0) + pp_data = in.dt[ppsnp_row, ] + if (dim(pp_data)[1] == 0) { + ppsnp_row = in.dt[in.dt$LOG10P == max(in.dt$LOG10P), ] + pp_data = ppsnp_row[1, ] + } + } + + + message("Generating Plot") + if ("LD" %in% colnames(in.dt) && "LD_BIN" %in% colnames(in.dt)) { + c = ggplot2::ggplot(gene_sub, ggplot2::aes_string(x = "value", + y = "y_value")) + ggplot2::geom_line(ggplot2::aes_string(group = "GENE_NAME"), + size = 2) + ggplot2::theme_minimal() + + ggplot2::geom_text(data = plot_lab, + ggplot2::aes_string(x = "value", y = "y_value", label = "GENE_NAME"), + hjust = -0.1, vjust = 0.3, + size = gene_name_s) + + ggplot2::theme(axis.title.y = ggplot2::element_text(color = "transparent", size = 28), + axis.text.y = ggplot2::element_blank(), + axis.ticks.y = ggplot2::element_blank(), + panel.border = element_blank(), + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.line.x = element_line(colour = "#595A5C")) + + ggplot2::xlab(paste0("chromosome ", + chr_in, " position")) + ggplot2::coord_cartesian(xlim = c(start, + end), ylim = c(0, (max(gene_sub$y_value) + 0.25))) + b = ggplot2::ggplot(in.dt, ggplot2::aes_string(x = "POS", + y = "LOG10P", color = "LD_BIN")) + ggplot2::geom_point() + + ggplot2::scale_colour_manual(values = c(`1.0-0.8` = "#DC0000FF", # "#DB003F", #"red", + `0.8-0.6` = "#F39B7FFF", # "#F59D10", #"darkorange1", + `0.6-0.4` = "#00A087FF", # "#49A01D", #"green1", + `0.4-0.2` = "#4DBBD5FF", # "#1290D9", #"skyblue1", + `0.2-0.0` = "#3C5488FF", # "#4C81BF", #"navyblue", + `NA` = "#A2A3A4" # "grey" + ), + drop = FALSE) + + labs(color = bquote(LD~r^2)) + + ggplot2::theme(panel.border = element_blank(), + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.line.x = element_blank(), + axis.line.y = element_line(colour = "#595A5C"), + axis.title.x=element_blank(), + axis.text.x=element_blank(), + axis.ticks.x=element_blank()) + + # ggplot2::xlab("Chromosome Position") + + # ggplot2::ylab("-log10(p-value)") + + ggplot2::ylab(bquote(-log[10]~(p-value))) + + ggplot2::coord_cartesian(xlim = c(start, end), ylim = c(min(in.dt$LOG10P), + max(in.dt$LOG10P))) + } + else { + c = ggplot2::ggplot(gene_sub, ggplot2::aes_string(x = "value", + y = "y_value")) + ggplot2::geom_line(ggplot2::aes_string(group = "GENE_NAME"), + size = 2) + ggplot2::theme_minimal() + + ggplot2::geom_text(data = plot_lab, + ggplot2::aes_string(x = "value", y = "y_value", label = "GENE_NAME"), + hjust = -0.1, vjust = 0.3, + size = gene_name_s) + + ggplot2::theme(axis.title.y = ggplot2::element_blank(), #ggplot2::element_text(color = "white", size = 28), + axis.text.y = ggplot2::element_blank(), + axis.ticks.y = ggplot2::element_blank(), + panel.border = element_blank(), + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.line.x = element_line(colour = "#595A5C")) + + ggplot2::xlab(paste0("chromosome ", + chr_in, " position")) + ggplot2::coord_cartesian(xlim = c(start, + end), ylim = c(0, (max(gene_sub$y_value) + 0.25))) + b = ggplot2::ggplot(in.dt, ggplot2::aes_string(x = "POS", + y = "LOG10P")) + ggplot2::geom_point() + ggplot2::theme(panel.border = element_blank(), + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + axis.line.x = element_blank(), + axis.line.y = element_line(colour = "#595A5C"), + axis.title.x=element_blank(), + axis.text.x=element_blank(), + axis.ticks.x=element_blank()) + + # ggplot2::xlab("Chromosome Position") + + # ggplot2::ylab("-log10(p-value)") + + ggplot2::ylab(bquote(-log[10]~(p-value))) + + ggplot2::coord_cartesian(xlim = c(start, end), ylim = c(min(in.dt$LOG10P), + max(in.dt$LOG10P))) + } + if (label_lead == TRUE) { + b = b + geom_point(data = label_data, + aes_string(x = "POS", + y = "LOG10P"), + color = "#8491B4FF", # "#9A3480", #"purple") + fill = "#8491B4FF", # "#9A3480", + size = 4, shape = 23) + + b = b + geom_text(data = label_data, + aes_string(label = "RS_ID"), + color = "black", + size = 4, hjust = 1.25) + } + if (grey_colors == TRUE) { + b = b + geom_point(color = "#A2A3A4", fill = "#A2A3A4") + } + + if (cred_set == TRUE) { + + b = b + geom_point(data = pp_data, + aes_string(x = "POS", + y = "LOG10P")) + + geom_point(aes(colour = Posterior_Prob)) + + scale_colour_gradient( + low = "#F39B7FFF", # "#132B43", + high = "#DC0000FF", # "#56B1F7", + space = "Lab", + na.value = "#A2A3A4", # "grey50", + guide = "colourbar", + aesthetics = "colour" + ) + scale_fill_gradient( + low = "#F39B7FFF", # "#132B43", + high = "#DC0000FF", # "#56B1F7", + space = "Lab", + na.value = "#A2A3A4", # "grey50", + guide = "colourbar", + aesthetics = "colour" + ) + + } + + ggpubr::ggarrange(b, c, heights = c(gene_track_h, 1), nrow = 2, ncol = 1, + common.legend = TRUE, legend = "right") +} + + +################################################################################ +# MANHATTAN PLOTTING +################################################################################ +# based on the qqman package by Stephen Turner + + +manhattan_uu <- function (x, chr = "CHR", bp = "BP", p = "P", snp = "SNP", col = c("gray10", "gray60"), chrlabs = NULL, suggestiveline = -log10(1e-05), + genomewideline = -log10(5e-08), highlight = NULL, logp = TRUE, + annotatePval = NULL, annotateTop = TRUE, ...) { + CHR = BP = P = index = NULL + if (!(chr %in% names(x))) + stop(paste("Column", chr, "not found!")) + if (!(bp %in% names(x))) + stop(paste("Column", bp, "not found!")) + if (!(p %in% names(x))) + stop(paste("Column", p, "not found!")) + if (!(snp %in% names(x))) + warning(paste("No SNP column found. OK unless you're trying to highlight.")) + if (!is.numeric(x[[chr]])) + stop(paste(chr, "column should be numeric. Do you have 'X', 'Y', 'MT', etc? If so change to numbers and try again.")) + if (!is.numeric(x[[bp]])) + stop(paste(bp, "column should be numeric.")) + if (!is.numeric(x[[p]])) + stop(paste(p, "column should be numeric.")) + if (!is.null(x[[snp]])) + d = data.frame(CHR = x[[chr]], BP = x[[bp]], P = x[[p]], + pos = NA, index = NA, SNP = x[[snp]], stringsAsFactors = FALSE) + else d = data.frame(CHR = x[[chr]], BP = x[[bp]], P = x[[p]], + pos = NA, index = NA) + d <- d[order(d$CHR, d$BP), ] + if (logp) { + d$logp <- -log10(d$P) + } + else { + d$logp <- d$P + } + d$index = rep.int(seq_along(unique(d$CHR)), times = tapply(d$SNP, + d$CHR, length)) + nchr = length(unique(d$CHR)) + if (nchr == 1) { + d$pos = d$BP + xlabel = paste("Chromosome", unique(d$CHR), "position") + } + else { + lastbase = 0 + ticks = NULL + for (i in unique(d$index)) { + if (i == 1) { + d[d$index == i, ]$pos = d[d$index == i, ]$BP + } + else { + lastbase = lastbase + max(d[d$index == (i - 1), + "BP"]) + d[d$index == i, "BP"] = d[d$index == i, "BP"] - + min(d[d$index == i, "BP"]) + 1 + d[d$index == i, "pos"] = d[d$index == i, "BP"] + + lastbase + } + } + ticks <- tapply(d$pos, d$index, quantile, probs = 0.5) + xlabel = "Chromosome" + labs <- unique(d$CHR) + } + xmax = ceiling(max(d$pos) * 1.03) + xmin = floor(max(d$pos) * -0.03) + def_args <- list(xaxt = "n", bty = "n", xaxs = "i", yaxs = "i", + las = 1, pch = 20, xlim = c(xmin, xmax), ylim = c(0, + ceiling(max(d$logp))), xlab = xlabel, ylab = expression(-log[10](italic(p)))) + dotargs <- list(...) + do.call("plot", c(NA, dotargs, def_args[!names(def_args) %in% + names(dotargs)])) + if (!is.null(chrlabs)) { + if (is.character(chrlabs)) { + if (length(chrlabs) == length(labs)) { + labs <- chrlabs + } + else { + warning("You're trying to specify chromosome labels but the number of labels != number of chromosomes.") + } + } + else { + warning("If you're trying to specify chromosome labels, chrlabs must be a character vector") + } + } + if (nchr == 1) { + axis(1, ...) + } + else { + axis(1, at = ticks, labels = labs, ...) + } + col = rep_len(col, max(d$index)) + if (nchr == 1) { + with(d, points(pos, logp, pch = 20, col = col[1], ...)) + } + else { + icol = 1 + for (i in unique(d$index)) { + points(d[d$index == i, "pos"], d[d$index == i, "logp"], + col = col[icol], pch = 20, ...) + icol = icol + 1 + } + } + if (suggestiveline) + # abline(h = suggestiveline, col = "blue") # original + abline(h = suggestiveline, col = "#595A5C", lty = "dashed") # original + if (genomewideline) + # abline(h = genomewideline, col = "red") # original + abline(h = genomewideline, col = "#E55738", lty = "dashed") # original + if (!is.null(highlight)) { + if (any(!(highlight %in% d$SNP))) + warning("You're trying to highlight SNPs that don't exist in your results.") + d.highlight = d[which(d$SNP %in% highlight), ] + # with(d.highlight, points(pos, logp, col = "green3", pch = 20, ...)) # original + with(d.highlight, points(pos, logp, col = "#9FC228", pch = 20, ...)) + } + if (!is.null(annotatePval)) { + if (logp) { + topHits = subset(d, P <= annotatePval) + } + else topHits = subset(d, P >= annotatePval) + par(xpd = TRUE) + if (annotateTop == FALSE) { + if (logp) { + with(subset(d, P <= annotatePval), textxy(pos, + -log10(P), offset = 0.625, labs = topHits$SNP, + cex = 0.45), ...) + } + else with(subset(d, P >= annotatePval), textxy(pos, + P, offset = 0.625, labs = topHits$SNP, cex = 0.45), + ...) + } + else { + topHits <- topHits[order(topHits$P), ] + topSNPs <- NULL + for (i in unique(topHits$CHR)) { + chrSNPs <- topHits[topHits$CHR == i, ] + topSNPs <- rbind(topSNPs, chrSNPs[1, ]) + } + if (logp) { + textxy(topSNPs$pos, -log10(topSNPs$P), offset = 0.625, + labs = topSNPs$SNP, cex = 0.5, ...) + } + else textxy(topSNPs$pos, topSNPs$P, offset = 0.625, + labs = topSNPs$SNP, cex = 0.5, ...) + } + } + par(xpd = FALSE) +} \ No newline at end of file diff --git a/Scripts/local.system.R b/Scripts/local.system.R new file mode 100644 index 0000000..1b81417 --- /dev/null +++ b/Scripts/local.system.R @@ -0,0 +1,99 @@ +################################################################################ +# LOCAL SYSTEM # +################################################################################ + +### Operating System Version +### MacBook Pro +# ROOT_loc = "/Users/swvanderlaan" +# STORAGE_loc = "/Users/swvanderlaan" +# CLOUD_loc = "/Users/swvanderlaan/Library/Mobile Documents/com~apple~CloudDocs/" +# ONEDRIVE_loc = "/Users/swvanderlaan/Library/CloudStorage/OneDrive-UMCUtrecht/Genomics" + +### MacBook Air +ROOT_loc = "/Users/slaan3" +STORAGE_loc = "/Users/slaan3" +CLOUD_loc = "/Users/slaan3/Library/Mobile Documents/com~apple~CloudDocs/" +ONEDRIVE_loc = "/Users/slaan3/Library/CloudStorage/OneDrive-UMCUtrecht/Genomics" + +# STORAGE_loc = "/Volumes/LaCie" + +### Generic +LAB_loc = paste0(CLOUD_loc, "/Genomics/LabBusiness") + +AEDB_loc = paste0(ONEDRIVE_loc, "/Athero-Express/AE-AAA_GS_DBs") + +### Genetic and genomic data +PLINK_loc=paste0(STORAGE_loc,"/PLINK") +GWAS_loc=paste0(PLINK_loc,"/_GWAS_Datasets/_CHARGE_CAC") + +# genetic +AEGSQC_loc = paste0(PLINK_loc, "/_AE_ORIGINALS/AEGS_COMBINED_QC2018") +MICHIMP_loc=paste0(PLINK_loc,"/_AE_ORIGINALS/AEGS_COMBINED_EAGLE2_1000Gp3v5HRCr11") + +# sc rna +AESCRNA_loc = paste0(PLINK_loc, "/_AE_ORIGINALS/AESCRNA/prepped_data") + +# bulk rna +AERNA_loc = paste0(PLINK_loc, "/_AE_ORIGINALS/AERNA") + +### Project +# PROJECT_loc = paste0(PLINK_loc, "/analyses/grants/telomeregrant2022") +PROJECT_loc = paste0(STORAGE_loc, "/git/CirculatoryHealth/Asympt_vs_Ocular") + +# use this if there is relevant information here. +ifelse(!dir.exists(file.path(PROJECT_loc, "/targets")), + dir.create(file.path(PROJECT_loc, "/targets")), + FALSE) +TARGET_loc = paste0(PROJECT_loc,"/targets") + +### SOME VARIABLES WE NEED DOWN THE LINE +TRAIT_OF_INTEREST = "PCSK9" # Phenotype +PROJECTNAME = "PCSK9" + +cat("\nCreate a new analysis directories.\n") + +cat("\n- general directory\n") +ifelse(!dir.exists(file.path(PROJECT_loc)), + dir.create(file.path(PROJECT_loc)), + FALSE) +ANALYSIS_loc = paste0(PROJECT_loc) + +cat("\n- for plots\n") +ifelse(!dir.exists(file.path(ANALYSIS_loc, "/PLOTS")), + dir.create(file.path(ANALYSIS_loc, "/PLOTS")), + FALSE) +PLOT_loc = paste0(ANALYSIS_loc,"/PLOTS") + +ifelse(!dir.exists(file.path(PLOT_loc, "/QC")), + dir.create(file.path(PLOT_loc, "/QC")), + FALSE) +QC_loc = paste0(PLOT_loc,"/QC") + +cat("\n- for output of summary results\n") +ifelse(!dir.exists(file.path(ANALYSIS_loc, "/OUTPUT")), + dir.create(file.path(ANALYSIS_loc, "/OUTPUT")), + FALSE) +OUT_loc = paste0(ANALYSIS_loc, "/OUTPUT") + +cat("\n- for baseline tables\n") +ifelse(!dir.exists(file.path(ANALYSIS_loc, "/BASELINE")), + dir.create(file.path(ANALYSIS_loc, "/BASELINE")), + FALSE) +BASELINE_loc = paste0(ANALYSIS_loc, "/BASELINE") + +cat("\n- for genetic analyses\n") +ifelse(!dir.exists(file.path(ANALYSIS_loc, "/SNP")), + dir.create(file.path(ANALYSIS_loc, "/SNP")), + FALSE) +SNP_loc = paste0(ANALYSIS_loc, "/SNP") + +cat("\n- for Cox regression results\n") +ifelse(!dir.exists(file.path(PLOT_loc, "/COX")), + dir.create(file.path(PLOT_loc, "/COX")), + FALSE) +COX_loc = paste0(PLOT_loc, "/COX") + + +setwd(paste0(PROJECT_loc)) +getwd() +list.files() \ No newline at end of file diff --git a/Scripts/pack01.packages.R b/Scripts/pack01.packages.R new file mode 100644 index 0000000..6340bde --- /dev/null +++ b/Scripts/pack01.packages.R @@ -0,0 +1,50 @@ +################################################################################ +# PACKAGES TO LOAD # +################################################################################ + +cat("\n* General packages...\n") +install.packages.auto("credentials") +library("credentials") +credentials::set_github_pat() + +install.packages.auto("R.utils") + +install.packages.auto("worcs") + +install.packages.auto("readr") +install.packages.auto("optparse") +install.packages.auto("tools") +install.packages.auto("dplyr") +install.packages.auto("tidyr") +install.packages.auto("naniar") + +# To get 'data.table' with 'fwrite' to be able to directly write gzipped-files +# Ref: https://stackoverflow.com/questions/42788401/is-possible-to-use-fwrite-from-data-table-with-gzfile +# install.packages("data.table", repos = "https://Rdatatable.gitlab.io/data.table") +library(data.table) + +install.packages.auto("tidyverse") +install.packages.auto("knitr") +install.packages.auto("DT") +install.packages.auto("eeptools") + +install.packages.auto("haven") +install.packages.auto("tableone") + +install.packages.auto("BlandAltmanLeh") + +# Install the devtools package from Hadley Wickham +install.packages.auto('devtools') + +# for plotting +install.packages.auto("pheatmap") +install.packages.auto("forestplot") +install.packages.auto("ggplot2") + +install.packages.auto("ggpubr") + +install.packages.auto("UpSetR") + +devtools::install_github("thomasp85/patchwork") +library("patchwork") +install.packages.auto("sjPlot") diff --git a/Scripts/pack02.packages.R b/Scripts/pack02.packages.R new file mode 100644 index 0000000..192cd88 --- /dev/null +++ b/Scripts/pack02.packages.R @@ -0,0 +1,91 @@ +################################################################################ +# PACKAGES TO LOAD # +################################################################################ + +cat("\n* General packages...\n") +install.packages.auto("credentials") +library("credentials") +# credentials::set_github_pat() + +install.packages.auto("R.utils") + +install.packages.auto('pander') +install.packages.auto('openxlsx') + +install.packages.auto("readr") +install.packages.auto("optparse") +install.packages.auto("tools") +install.packages.auto("dplyr") +install.packages.auto("tidyr") +install.packages.auto("tidylog") +library("tidylog", warn.conflicts = FALSE) +install.packages.auto("naniar") + +# To get 'data.table' with 'fwrite' to be able to directly write gzipped-files +# Ref: https://stackoverflow.com/questions/42788401/is-possible-to-use-fwrite-from-data-table-with-gzfile +# install.packages("data.table", repos = "https://Rdatatable.gitlab.io/data.table") +library(data.table) + +install.packages.auto("tidyverse") +install.packages.auto("knitr") +install.packages.auto("DT") + +# for plotting +install.packages.auto("qqman") +install.packages.auto("forestplot") +install.packages.auto("pheatmap") +# for meta-analysis +install.packages.auto("meta") +install.packages.auto("bacon") + +install.packages.auto("reshape2") + +install.packages.auto("ggpubr") +install.packages.auto("patchwork") +install.packages.auto("corrr") + +install.packages.auto("haven") +install.packages.auto("tableone") + +# Install the devtools package from Hadley Wickham +install.packages.auto('devtools') + +cat("\n* Genomic packages...\n") +install.packages.auto("GenomicFeatures") +install.packages.auto("GenomicRanges") +install.packages.auto("SummarizedExperiment") +install.packages.auto("DESeq2") +install.packages.auto("org.Hs.eg.db") +install.packages.auto("mygene") +install.packages.auto("TxDb.Hsapiens.UCSC.hg19.knownGene") +install.packages.auto("org.Hs.eg.db") +install.packages.auto("AnnotationDbi") + +# required for EnsDb.Hsapiens.v86 +# install.packages("minqa") + +# install.packages.auto("EnsDb.Hsapiens.v86") +# if (!require("BiocManager", quietly = TRUE)) +# install.packages("BiocManager") +# +# BiocManager::install("EnsDb.Hsapiens.v86") +library("EnsDb.Hsapiens.v86") + +install.packages.auto("EnhancedVolcano") + +# Install the annotation tables +library("devtools") +# devtools::install_github("stephenturner/annotables") +library(dplyr) +library(annotables) + +# alternative chart of a correlation matrix +# -------------------------------- +# Alternative solution https://www.r-graph-gallery.com/199-correlation-matrix-with-ggally.html +# install.packages.auto("GGally") + +# Quick display of two cabapilities of GGally, to assess the distribution and correlation of variables +library(GGally) + + + diff --git a/Scripts/pack03.packages.R b/Scripts/pack03.packages.R new file mode 100644 index 0000000..5b6a2ec --- /dev/null +++ b/Scripts/pack03.packages.R @@ -0,0 +1,47 @@ +################################################################################ +# PACKAGES TO LOAD # +################################################################################ + +install.packages.auto("readr") +install.packages.auto("optparse") +install.packages.auto("tools") +install.packages.auto("dplyr") +install.packages.auto("tidyr") +install.packages.auto("tidylog") +library("tidylog", warn.conflicts = FALSE) +install.packages.auto("naniar") + +# To get 'data.table' with 'fwrite' to be able to directly write gzipped-files +# Ref: https://stackoverflow.com/questions/42788401/is-possible-to-use-fwrite-from-data-table-with-gzfile +# install.packages("data.table", repos = "https://Rdatatable.gitlab.io/data.table") +library(data.table) + +install.packages.auto("tidyverse") +install.packages.auto("knitr") +install.packages.auto("DT") + +install.packages.auto("org.Hs.eg.db") +install.packages.auto("mygene") +install.packages.auto("EnhancedVolcano") + +install.packages.auto("haven") +install.packages.auto("tableone") + +# For a more efficient implementation of the Wilcoxon Rank Sum Test, +# (default method for FindMarkers) please install the limma package +# -------------------------------------------- +install.packages('BiocManager') +BiocManager::install('limma') +# -------------------------------------------- +# After installation of limma, Seurat will automatically use the more +# efficient implementation (no further action necessary). +# This message will be shown once per session + +# Install the devtools package from Hadley Wickham +install.packages.auto('devtools') +# Replace '2.3.4' with your desired version +# devtools::install_version(package = 'Seurat', version = package_version('2.3.4')) +install.packages.auto("Seurat") +library("Seurat") + + diff --git a/images/AE_Genomics_2010.png b/images/AE_Genomics_2010.png new file mode 100755 index 0000000..bb2425a Binary files /dev/null and b/images/AE_Genomics_2010.png differ diff --git a/images/ERA_CVD_Logo_CMYK.png b/images/ERA_CVD_Logo_CMYK.png new file mode 100644 index 0000000..ce58b63 Binary files /dev/null and b/images/ERA_CVD_Logo_CMYK.png differ diff --git a/images/leducq-logo-large.png b/images/leducq-logo-large.png new file mode 100755 index 0000000..ec8df58 Binary files /dev/null and b/images/leducq-logo-large.png differ diff --git a/images/leducq-logo-small.png b/images/leducq-logo-small.png new file mode 100755 index 0000000..ccc774b Binary files /dev/null and b/images/leducq-logo-small.png differ diff --git a/images/to_aition.png b/images/to_aition.png new file mode 100644 index 0000000..8268e3e Binary files /dev/null and b/images/to_aition.png differ diff --git a/images/worcs_icon.png b/images/worcs_icon.png new file mode 100644 index 0000000..2e54ae4 Binary files /dev/null and b/images/worcs_icon.png differ diff --git a/prepare_data.R b/prepare_data.R new file mode 100644 index 0000000..4b0396f --- /dev/null +++ b/prepare_data.R @@ -0,0 +1,6 @@ +# In this file, write the R-code necessary to load your original data file +# (e.g., an SPSS, Excel, or SAS-file), and convert it to a data.frame. 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"Requirements": [ + "xfun" + ] + }, + "urlchecker": { + "Package": "urlchecker", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "409328b8e1253c8d729a7836fe7f7a16", + "Requirements": [ + "cli", + "curl", + "xml2" + ] + }, + "usethis": { + "Package": "usethis", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a67a22c201832b12c036cc059f1d137d", + "Requirements": [ + "cli", + "clipr", + "crayon", + "curl", + "desc", + "fs", + "gert", + "gh", + "glue", + "jsonlite", + "lifecycle", + "purrr", + "rappdirs", + "rlang", + "rprojroot", + "rstudioapi", + "whisker", + "withr", + "yaml" + ] + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c9c462b759a5cc844ae25b5942654d13", + "Requirements": [] + }, + "uwot": { + "Package": "uwot", + "Version": "0.1.14", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c40f4dbc76dd87140045b37a3150a0f1", + "Requirements": [ + "FNN", + "Matrix", + "Rcpp", + "RcppAnnoy", + "RcppProgress", + "dqrng", + "irlba" + ] + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0e3dfc070b2a8f0478fcdf86fb33355d", + "Requirements": [ + "cli", + "glue", + "rlang" + ] + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "62f4b5da3e08d8e5bcba6cac15603f70", + "Requirements": [] + }, + "waldo": { + "Package": "waldo", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "035fba89d0c86e2113120f93301b98ad", + "Requirements": [ + "cli", + "diffobj", + "fansi", + "glue", + "rematch2", + "rlang", + "tibble" + ] + }, + "whisker": { + "Package": "whisker", + "Version": "0.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ca970b96d894e90397ed20637a0c1bbe", + "Requirements": [] + }, + "withr": { + "Package": "withr", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c0e49a9760983e81e55cdd9be92e7182", + "Requirements": [] + }, + "worcs": { + "Package": "worcs", + "Version": "0.1.10", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d6f0b99aebde4d2c30ca73e09686fbd2", + "Requirements": [ + "credentials", + "digest", + "gert", + "gh", + "prereg", + "ranger", + "renv", + "rmarkdown", + "rticles", + "tinytex", + "usethis", + "yaml" + ] + }, + "xfun": { + "Package": "xfun", + "Version": "0.34", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9eba2411b0b1f879797141bd24df7407", + "Requirements": [] + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "40682ed6a969ea5abfd351eb67833adc", + "Requirements": [] + }, + "xopen": { + "Package": "xopen", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Requirements": [ + "processx" + ] + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", + "Requirements": [] + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9b570515751dcbae610f29885e025b41", + "Requirements": [] + }, + "zip": { + "Package": "zip", + "Version": "2.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a7e91189fa51d9029a30eba3831ce53f", + "Requirements": [] + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.42.0", + "Source": "Bioconductor", + "git_url": "https://git.bioconductor.org/packages/zlibbioc", + "git_branch": "RELEASE_3_15", + "git_last_commit": "aa074d7", + "git_last_commit_date": "2022-04-26", + "Hash": "908694d02f7332d0576e7c881e572c5a", + "Requirements": [] + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-11", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "874a5b77fe0cfacf2a3450069ae70926", + "Requirements": [ + "lattice" + ] + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..019b5a6 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,994 @@ + +local({ + + # the requested version of renv + version <- "0.16.0" + + # the project directory + project <- getwd() + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + if (!enabled) + return(FALSE) + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.environment(x) || length(x)) x else y + } + + bootstrap <- function(version, library) { + + # attempt to download renv + tarball <- tryCatch(renv_bootstrap_download(version), error = identity) + if (inherits(tarball, "error")) + stop("failed to download renv ", version) + + # now attempt to install + status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) + if (inherits(status, "error")) + stop("failed to install renv ", version) + + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) + return(repos) + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # if we're testing, re-use the test repositories + if (renv_bootstrap_tests_running()) + return(getOption("renv.tests.repos")) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- getOption( + "renv.repos.cran", + "https://cloud.r-project.org" + ) + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + # if the renv version number has 4 components, assume it must + # be retrieved via github + nv <- numeric_version(version) + components <- unclass(nv)[[1]] + + # if this appears to be a development version of 'renv', we'll + # try to restore from github + dev <- length(components) == 4L + + # begin collecting different methods for finding renv + methods <- c( + renv_bootstrap_download_tarball, + if (dev) + renv_bootstrap_download_github + else c( + renv_bootstrap_download_cran_latest, + renv_bootstrap_download_cran_archive + ) + ) + + for (method in methods) { + path <- tryCatch(method(version), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("failed to download renv ", version) + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + message("* Downloading renv ", version, " ... ", appendLF = FALSE) + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) { + message("FAILED") + return(FALSE) + } + + # report success and return + message("OK (downloaded ", type, ")") + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + message("* Downloading renv ", version, " ... ", appendLF = FALSE) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) { + message("OK") + return(destfile) + } + + } + + message("FAILED") + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + info <- file.info(tarball, extra_cols = FALSE) + if (identical(info$isdir, TRUE)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + fmt <- "* Bootstrapping with tarball at path '%s'." + msg <- sprintf(fmt, tarball) + message(msg) + + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) { + message("FAILED") + return(FALSE) + } + + message("OK") + return(destfile) + + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + message("* Installing renv ", version, " ... ", appendLF = FALSE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + r <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + output <- system2(r, args, stdout = TRUE, stderr = TRUE) + message("Done!") + + # check for successful install + status <- attr(output, "status") + if (is.numeric(status) && !identical(status, 0L)) { + header <- "Error installing renv:" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- c(header, lines, output) + writeLines(text, con = stderr()) + } + + status + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version) { + + loadedversion <- utils::packageDescription("renv", fields = "Version") + if (version == loadedversion) + return(TRUE) + + # assume four-component versions are from GitHub; three-component + # versions are from CRAN + components <- strsplit(loadedversion, "[.-]")[[1]] + remote <- if (length(components) == 4L) + paste("rstudio/renv", loadedversion, sep = "@") + else + paste("renv", loadedversion, sep = "@") + + fmt <- paste( + "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", + "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", + "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", + sep = "\n" + ) + + msg <- sprintf(fmt, loadedversion, version, remote) + warning(msg, call. = FALSE) + + FALSE + + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + + renv_json_read <- function(file = NULL, text = NULL) { + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) + renv_json_read_jsonlite(file, text) + else + renv_json_read_default(file, text) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% read(file), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% read(file), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # attempt to load + if (renv_bootstrap_load(project, libpath, version)) + return(TRUE) + + # load failed; inform user we're about to bootstrap + prefix <- paste("# Bootstrapping renv", version) + postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") + header <- paste(prefix, postfix) + message(header) + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + message("* Successfully installed and loaded renv ", version, ".") + return(renv::load()) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + +}) diff --git a/renv/settings.dcf b/renv/settings.dcf new file mode 100644 index 0000000..169d82f --- /dev/null +++ b/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: implicit +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE diff --git a/run_me.R b/run_me.R new file mode 100644 index 0000000..40c0d44 --- /dev/null +++ b/run_me.R @@ -0,0 +1,6 @@ +library("worcs") +# We recommend that you prepare your raw data for analysis in 'prepare_data.R', +# and end that file with either open_data(yourdata), or closed_data(yourdata). +# Then, uncomment the line below to load the original or synthetic data +# (whichever is available), to allow anyone to reproduce your code: +# load_data()