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| # Spatial distribution | ||
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| Color by: | ||
| * sample metadata | ||
| * time isolated/submitted | ||
| * gene content | ||
| * relatedness |
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| # Quality control | ||
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| * A quick indicator of status of each step. | ||
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| ## Input data quality | ||
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| * multiqc link | ||
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| ## Downloaded references | ||
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| * quast | ||
| * table with rows for each sample with info on references chosen | ||
| - sample id | ||
| - reference id | ||
| - ANI between sample and reference | ||
| * table with one row per reference (taxon id, GSA id, classification, link to ncbi) | ||
| * sourmash output (tree?) | ||
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| ## Assembly and annotation | ||
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| * depth of coverage | ||
| * quast link | ||
| * BUSCO gene content? | ||
| * bakta output? | ||
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| ## Variant calling? | ||
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| * vcfr for plots | ||
| * iqtree model selection, number of informative sites, indels | ||
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| ## Core genome phylogeny | ||
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| * core gene info (how many genes, length, paralogs) | ||
| * outlier samples causing few genes to be chosen | ||
| * iqtree model selection, number of informative sites, indels |
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| ## Software used | ||
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| ```{r include=FALSE} | ||
| # automatically create a bib database for R packages | ||
| knitr::write_bib(c( | ||
| .packages(), 'bookdown', 'knitr', 'rmarkdown' | ||
| ), 'packages.bib') | ||
| ``` | ||
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| `r if (knitr::is_html_output()) ' | ||
| # References {-} | ||
| '` |
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| --- | ||
| title: "Pathogensurveillance Report" | ||
| date: "`r Sys.Date()`" | ||
| site: bookdown::bookdown_site | ||
| documentclass: book | ||
| bibliography: [book.bib, packages.bib] | ||
| # url: your book url like https://bookdown.org/yihui/bookdown | ||
| # cover-image: path to the social sharing image like images/cover.jpg | ||
| description: | | ||
| A report generated by the Pathogensurveillance genome analysis pipeline. | ||
| link-citations: yes | ||
| github-repo: rstudio/bookdown-demo | ||
| params: | ||
| samp_data: "/media/fosterz/external_primary/files/projects/work/current/pathogensurveillance/test/data/metadata_medium.csv" | ||
| ref_data: "/media/fosterz/external_primary/files/projects/work/current/pathogensurveillance/work/60/71f547293aa5d22f469ea3ee215581/merged_assembly_stats.tsv" | ||
| snp_phylos: "/media/fosterz/external_primary/files/projects/work/current/pathogensurveillance/work/60/71f547293aa5d22f469ea3ee215581/xan_test_22_331_assembly.treefile" | ||
| ani_matrix: "/media/fosterz/external_primary/files/projects/work/current/pathogensurveillance/work/60/71f547293aa5d22f469ea3ee215581/comp.csv" | ||
| core_phylo: "/media/fosterz/external_primary/files/projects/work/current/pathogensurveillance/work/60/71f547293aa5d22f469ea3ee215581/xan_test.treefile" | ||
| --- | ||
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| # Run info | ||
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| This is the first page a user sees. | ||
| What should go here? | ||
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| ## Input settings | ||
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| ## Software used | ||
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| ```{r include=FALSE} | ||
| # automatically create a bib database for R packages | ||
| knitr::write_bib(c( | ||
| .packages(), 'bookdown', 'knitr', 'rmarkdown' | ||
| ), 'packages.bib') | ||
| ``` | ||
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| <!--chapter:end:index.Rmd--> | ||
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| # Identification | ||
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| ```{r include=FALSE, eval=FALSE} | ||
| work_dir = "/media/fosterz/external_primary/files/projects/work/current/nf-core-plantpathsurveil/work/60/71f547293aa5d22f469ea3ee215581" | ||
| params = list( | ||
| samp_data = "metadata_medium.csv", | ||
| ref_data = "merged_assembly_stats.tsv", | ||
| snp_phylos = list("xan_test_22_331_assembly.treefile"), | ||
| ani_matrix = "comp.csv", | ||
| core_phylo = "xan_test.treefile" | ||
| ) | ||
| params = lapply(params, function(x) file.path(work_dir, x)) | ||
| ``` | ||
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| ```{r id_setup, include=FALSE} | ||
| knitr::opts_chunk$set(echo = FALSE, fig.width = 10, warning = FALSE) | ||
| ``` | ||
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| ```{r id_libraries} | ||
| library(phylocanvas) | ||
| library(ape) | ||
| library(magrittr) | ||
| ``` | ||
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| ```{r id_parse_inputs} | ||
| ref_meta <- read.csv(params$ref_data, sep = '\t') | ||
| ref_meta$modified_id <- gsub(ref_meta$LastMajorReleaseAccession, pattern = ".", replacement = "_", fixed = TRUE) | ||
| samp_meta <- read.csv(params$samp_data, sep = ',') | ||
| samp_meta$modified_id <- paste0(gsub(samp_meta$sample, pattern = "-", replacement = "_", fixed = TRUE), "_T1") | ||
| ani_matrix <- read.csv(params$ani_matrix, sep = ',', check.names = FALSE) | ||
| core_tree <- ape::read.tree(params$core_phylo) | ||
| snp_trees <- ape::read.tree(params$snp_phylos) | ||
| ``` | ||
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| ## Initial ANI tree | ||
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| ## Core genome phylogeny | ||
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| ```{r id_core_phylo, fig.height = 7, eval = ! is.null(core_tree)} | ||
| # Identify which tips are samples and references | ||
| sample_ids <- core_tree$tip.label[core_tree$tip.label %in% samp_meta$modified_id] | ||
| # Root tree | ||
| colnames(ani_matrix) <- gsub(colnames(ani_matrix), pattern = "[.-]", replacement = "_") | ||
| rownames(ani_matrix) <- colnames(ani_matrix) | ||
| group_ani <- ani_matrix[rownames(ani_matrix) %in% core_tree$tip.label, colnames(ani_matrix) %in% core_tree$tip.label] | ||
| core_tree <- root(core_tree, names(which.min(colMeans(group_ani[sample_ids, ])))) | ||
| # Set tip labels to taxon names for reference sequences | ||
| # TODO: need a more reliable way to get IDs | ||
| name_key <- c( | ||
| ref_meta$Organism, | ||
| samp_meta$sample | ||
| ) | ||
| names(name_key) <- c( | ||
| ref_meta$modified_id, | ||
| samp_meta$modified_id | ||
| ) | ||
| core_tree$tip.label <- name_key[core_tree$tip.label] | ||
| # Plot tree | ||
| phycanv <- phylocanvas(core_tree, treetype = "rectangular", alignlabels = T, showscalebar = T, width = "100%") | ||
| for (x in name_key[sample_ids]) { | ||
| phycanv <- style_node(phycanv, x, labelcolor = "green", labeltextsize = 30) | ||
| } | ||
| phycanv | ||
| ``` | ||
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| ```{asis id_no_core_phylo, echo = is.null(core_tree)} | ||
| There is no tree to draw, probably because there were too few samples. | ||
| More info will be added later. | ||
| ``` | ||
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| <!--chapter:end:01-identification.Rmd--> | ||
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| # Diversity | ||
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| ```{r include=FALSE, eval=FALSE} | ||
| work_dir = "/media/fosterz/external_primary/files/projects/work/current/nf-core-plantpathsurveil/work/60/71f547293aa5d22f469ea3ee215581" | ||
| params = list( | ||
| samp_data = "metadata_medium.csv", | ||
| ref_data = "merged_assembly_stats.tsv", | ||
| snp_phylos = list("xan_test_22_331_assembly.treefile"), | ||
| ani_matrix = "comp.csv", | ||
| core_phylo = "xan_test.treefile" | ||
| ) | ||
| params = lapply(params, function(x) file.path(work_dir, x)) | ||
| ``` | ||
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| ```{r div_setup, include=FALSE} | ||
| knitr::opts_chunk$set(echo = FALSE, fig.width = 10, warning = FALSE) | ||
| ``` | ||
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| ```{r div_libraries} | ||
| library(phylocanvas) | ||
| library(ape) | ||
| ``` | ||
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| ```{r div_parse_inputs} | ||
| ref_meta <- read.csv(params$ref_data, sep = '\t') | ||
| ref_meta$modified_id <- gsub(ref_meta$LastMajorReleaseAccession, pattern = ".", replacement = "_", fixed = TRUE) | ||
| samp_meta <- read.csv(params$samp_data, sep = ',') | ||
| samp_meta$modified_id <- paste0(gsub(samp_meta$sample, pattern = "-", replacement = "_", fixed = TRUE), "_T1") | ||
| ani_matrix <- read.csv(params$ani_matrix, sep = ',', check.names = FALSE) | ||
| core_tree <- ape::read.tree(params$core_phylo) | ||
| snp_trees <- ape::read.tree(params$snp_phylos) | ||
| ``` | ||
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| ## SNP phylogeny | ||
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| ```{r div_snp_phylo, fig.height = 7, eval = ! is.null(snp_trees)} | ||
| # Root tree | ||
| snp_trees <- root(snp_trees, "REF") | ||
| # Plot tree | ||
| phycanv <- phylocanvas(snp_trees, treetype = "rectangular", alignlabels = T, showscalebar = T, width = "100%") | ||
| phycanv | ||
| ``` | ||
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| ```{asis div_no_snp_phylo, echo = is.null(snp_trees)} | ||
| There is no tree to draw, probably because there were too few samples. | ||
| More info will be added later. | ||
| ``` | ||
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| ## Minimum spanning network | ||
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| <!--chapter:end:02-diversity.Rmd--> | ||
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| # Gene content | ||
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| ## Antibotic resistance genes | ||
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| ## Effectors | ||
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| ## Plasmids | ||
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| ## User-defined genes | ||
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| <!--chapter:end:03-gene_content.Rmd--> | ||
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| `r if (knitr::is_html_output()) ' | ||
| # References {-} | ||
| '` | ||
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| <!--chapter:end:07-references.Rmd--> | ||
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