Mercurial > repos > goeckslab > clustering_spatialge
changeset 0:555ca19d07e6 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-st/tree/main/tools/spatialge commit 482b2e0e6ca7aaa789ba07b8cd689da9a01532ef
| author | goeckslab |
|---|---|
| date | Wed, 13 Aug 2025 19:32:19 +0000 |
| parents | |
| children | |
| files | clustering.xml macros.xml spatialGE_clust.R spatialGE_multiple_input.R spatialGE_single_input.R test-data/ST_mel3_rep1_counts.tsv test-data/ST_mel3_rep1_mapping.tsv test-data/STobj_filtered.rds test-data/STobj_lung5.rds test-data/STobj_lung6.rds test-data/STobj_raw.rds test-data/clustered_Lung5_fov_2.png test-data/clustered_Lung6_fov_4.png test-data/filtered_ST_mel3_rep1_counts.png test-data/thrane_clinical.csv test-data/unfiltered_ST_mel3_rep1_counts.png |
| diffstat | 16 files changed, 1948 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustering.xml Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,174 @@ +<tool id="clustering_spatialGE" name="spatialGE Spatially-Informed Clustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> + <description>Unsupervised spatially-informed clustering on spatialGE spatial transcriptomics data</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="spatialge_requirements"/> + + <command detect_errors="aggressive"><![CDATA[ + + ##-------------------------- + ## CLUSTERING + ##-------------------------- + + Rscript '$__tool_directory__/spatialGE_clust.R' + + --file '$file' + + #if $datatype == 'visium' + --visium + #end if + + #if $datatype == 'raw' + --raw + #end if + + #if $datatype == 'cosmx' + --cosmx + #end if + + #if $samples + --samples '$samples' + #end if + + #if $spatial_weight + --weight '$spatial_weight' + #end if + + --dist '$dist_metric' + + #if str($deepsplit.split_type) == 'logical_split': + --dslogical + --logical '$split_true' + #end if + + #if str($deepsplit.split_type) == 'numeric_split': + --dsnumeric + --numeric '$split_numeric' + #end if + + #if $ptsize + --ptsize '$ptsize' + #end if + + ]]></command> + <inputs> + <param name="file" type="data" format="rds" label="STlist.rds output from spatialGE preprocessing tool" /> + <param name="datatype" type="select" label="Original data type from spatialGE Preprocessing" > + <option value="visium">Visium</option> + <option value="raw">Raw Data</option> + <option value="cosmx">CosMX-SMI</option> + </param> + <param name="samples" type="text" optional="true" label="Sample(s) to perform clustering (comma separated list)" /> + <param name="spatial_weight" type="float" min="0" max="1" value="0.025" optional="true" label="Weight to be applied to spatial distances" /> + <param name="dist_metric" type="select" label="Distance metric options" > + <option value="euclidean" selected="true">Euclidean</option> + <option value="manhattan">Manhattan</option> + <option value="maximum">Maximum</option> + <option value="minkowski">Minkowski</option> + <option value="canberra">Canberra</option> + </param> + <conditional name="deepsplit"> + <param name="split_type" type="select" label="Optional: specify deepSplit parameter for cluster splitting sensitivity" > + <option value="no_split" selected="true">Do not change cluster sensitivity</option> + <option value="logical_split">Logical split: generally perform more sensitive clustering</option> + <option value="numeric_split">Numeric split: specify clustering sensitivity between 0-4</option> + </param> + <when value="no_split"> + </when> + <when value="logical_split"> + <param name="split_true" type="boolean" label="Switch to Yes for logical deepSplit" /> + </when> + <when value="numeric_split"> + <param name="split_numeric" type="float" min="0" max="4" label="Specify number between 0-4 for deepSplit (higher value equals higher sensitivity)" /> + </when> + </conditional> + <param name="ptsize" type="float" min="0" max="5" value="2.75" optional="true" label="Specify plot point size" /> + </inputs> + <outputs> + <collection name="cluster_plots" type="list" label="Cluster Plots"> + <discover_datasets pattern="__name_and_ext__" directory="./cluster_plots" ext="png" /> + <filter>cluster_plots['plot'] == "cluster_plots"</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="file" value="STobj_lung6.rds" /> + <param name="datatype" value="cosmx" /> + <param name="samples" value="Lung6_fov_4" /> + <output_collection name="cluster_plots" > + <element name="clustered_Lung6_fov_4" file="clustered_Lung6_fov_4.png" compare="sim_size" /> + </output_collection> + </test> + <test expect_num_outputs="1"> + <param name="file" value="STobj_lung5.rds" /> + <param name="datatype" value="cosmx" /> + <param name="samples" value="Lung5_fov_2" /> + <conditional name="deepsplit"> + <param name="split_type" value="logical_split" /> + <param name="split_true" value="TRUE" /> + </conditional> + <output_collection name="cluster_plots"> + <element name="clustered_Lung5_fov_2" file="clustered_Lung5_fov_2.png" compare="sim_size" /> + </output_collection> + </test> + </tests> + <help> + <![CDATA[ + **What it does** + + spatialGE is a tool designed for the analysis and visualization of spatially-resolved transcriptomics data. + + spatialGE Spatially-Informed Clustering is built to perform unsupervised spatially-informed clustering on the spots/cells of spatial transcriptomics data and the expression of the top variable genes. + This tool will take the output of `spatialGE Preprocessing` and calculate a distance (defaults to euclidean) between spots/cells based on spatial coordinates. + The distances are weighted and hierarchical clustering is performed on the sum of the weighted distance matrices. This allows for a better understanding + of the tissue architecture by identifying tissue niches/domains that are spatially cohesive, according to spot/cell clustering. + + **Input** + + Currently, the only accepted input is an .rds file as output by `spatialGE Preprocessing`. The preprocessing step creates an `STlist`, spatialGE's required data type. + Please first perform preprocessing to transform spatial transcriptomics data, then use the output **STlist.rds** file as input for this tool. + + It is also required to specify the original data type. Please select either Visium, Raw Data, or CosMX-SMI + as the data type corresponding to the `spatialGE Preprocessing` input. + + **Optional Settings** + + - Sample(s) to perform clustering (comma separated list): + + - To perform clustering and plotting on only a subset of samples from the STlist.rds file, input a comma-separated list of unique sample names matching those in the input file + - Visium Example: sample_094c,sample_094d + - Raw Data Example: ST_mel3_rep1,ST_mel2_rep1 + - CosMS-SMI Example: Lung5_fov_2,Lung5_fov_11 + + - Weight to be applied to spatial distances: + + - Any number between 0-1 indicating the weight to be applied to spatial distances. A weight closer to 0 indicates that little spatial information is used, and clustering relies on gene expression profiles. A weight closer to 1 indicates that spatial information is heavily used, with little reliance on gene expression. The default value here is 0.025, using mostly gene expression with a spatial smoothing effect. + + - Distance metric options: + + List of distance metric options from `wordspace::dist.matrix`. Different metrics compare expression profiles and spatial coordinates differently. + + - Euclidean (default) + - Manhattan + - Maximum + - Minkowski + - Canberra + + - deepSplit for cluster sensitivity: + + Choose between logical or numeric deepSplit to provide a rough control over sensitivity to cluster splitting. The higher the value (or if TRUE), the more and smaller clusters will be produced. + + - Logical: set deepSplit to TRUE, cluster sensitivity will increase + + - Numeric: control deepSplit between 0-4, closer to 4 indicate shigher cluster resolution + + - Specify plot point size: + + - Increase or decrease size of points when plotting, between 0-5. Defaults to 2.75. + + ]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,16 @@ +<macros> + <token name="@TOOL_VERSION@">1.2.2</token> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="spatialge_requirements"> + <requirements> + <container type="docker">quay.io/goeckslab/spatialge</container> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btac145</citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spatialGE_clust.R Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,125 @@ +# ------------------------------ +# Spatially-Informed Clustering +# ------------------------------ + +# Purpose: +# Group cells into tissue domains using hierarchical clustering on a weighted similarity matrix + +library(spatialGE) +library(optparse) +library(ggplot2) +library(tools) +library(dplyr) + +### Command Line Options + + +option_list <- list( + make_option(c("-f", "--file"), action = "store", default = NA, type = "character", + help = "STlist .rds file path from preprocessing"), + make_option(c("--visium"), action = "store_true", type = "logical", default = FALSE, + help = "Flag for Visium data"), + make_option(c("--raw"), action = "store_true", type = "logical", default = FALSE, + help = "Flag for raw data"), + make_option(c("--cosmx"), action = "store_true", type = "logical", default = FALSE, + help = "Flag for CosMX data"), + make_option(c("-s", "--samples"), action = "store", default = NULL, type = "character", + help = "Sample subset to perform clustering on"), + make_option(c("-w", "--weight"), action = "store", default = 0.025, type = "numeric", + help = "Weight to be applied to spatial distances between 0-1"), + make_option(c("-d", "--dist"), action = "store", default = "euclidean", type = "character", + help = "Distance metric to be used, all methods found in wordspace::dist.matrix"), + make_option(c("--dslogical"), action = "store_true", type = "logical", default = FALSE, + help = "Deepsplit logical flag"), + make_option(c("--logical"), action = "store", default = TRUE, type = "logical", + help = "Control cluster resolution, true will produce more clusters"), + make_option(c("--dsnumeric"), action = "store_true", type = "logical", default = FALSE, + help = "Deepsplit numeric flag"), + make_option(c("--numeric"), action = "store", default = 0, type = "numeric", + help = "control cluster resolution between 0-4, higher number will produce more clusters"), + make_option(c("-p", "--ptsize"), action = "store", default = 2.75, type = "numeric", + help = "Size of points on cluster plot") +) + +### Main + +# parse args +opt <- parse_args(OptionParser(option_list = option_list)) + +# read in ST data from spatialGE preprocessing +STdata <- readRDS(opt$file) + +message("Rds object successfully loaded") + +# if deepSplit flag is included, choose between logical or numeric +if (opt$logical) { + deepsplit <- opt$dslogical +} else if (opt$numeric) { + deepsplit <- opt$dsnumeric +} + +if (!is.null(opt$samples)) { + opt$samples <- strsplit(opt$samples, ",")[[1]] +} else if (is.null(opt$samples)) { + opt$samples <- NULL +} + +# perform data clustering on transformed data +clusters <- STclust(x = STdata, samples = opt$samples, ws = opt$weight, dist_metric = opt$dist, deepSplit = deepsplit) + +message("Unsupervised spatially-informed clustering has been performed") + +# transform S4 to list for easier slot access +S4toList <- function(obj) { + slot_names <- slotNames(obj) + structure(lapply(slot_names, slot, object = obj), names = slot_names) +} + +STdata <- S4toList(STdata) + +message("Transformed to S4 for slot name access") + +# depending on data input type, pull correct sample column +if (opt$visium) { + sample_col <- "sample_id" +} else if (opt$raw) { + sample_col <- "sampleID" +} else if (opt$cosmx) { + sample_col <- "sample_name" +} + + +if (!is.null(opt$samples)) { + samples <- STdata$sample_meta %>% pull(.data[[sample_col]]) %>% intersect(opt$samples) +} else { + samples <- STdata$sample_meta %>% pull(.data[[sample_col]]) +} + + +message("Sample names identified") + +# create cluster plot directory +if (!dir.exists("cluster_plots")) dir.create("cluster_plots") + +# iterate through each sample, generate a plot, and save +for (s in samples) { + + plot <- STplot(x = clusters, ws = opt$weight, ptsize = opt$ptsize, deepSplit = deepsplit, samples = s) + + message("Cluster plots generated") + + + #create unique plot file names based on sample name + + filename <- paste0("clustered_", s, ".png") + + #save plot to subdir + ggsave( + path = "./cluster_plots", + filename = filename, + bg = "white", + width = 12 + ) +} + +message("Cluster plots saved")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spatialGE_multiple_input.R Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,197 @@ +# ------------- +# Data Cleaning +# ------------- + +# MULTIPLE INPUT SCRIPT: +# Accepts multiple sample input for raw data and cosmx +# Accepts single and multiple sample input for Visium, due to spatial subdirectory + +# Purpose: +# Transform data into STlist, perform QC, log transform + +library(spatialGE) +library(optparse) +library(ggplot2) +library(tools) +library(fs) + + +### Command Line Options + +option_list <- list( + make_option(c("-c", "--counts"), action = "store", default = NA, type = "character", + help = "Path to count data file(s)"), + make_option(c("-s", "--spots"), action = "store", default = NULL, type = "character", + help = "Path to cell coordinates file(s), not required for Visium or Xenium"), + make_option(c("-m", "--meta"), action = "store", default = NA, type = "character", + help = "Path to metadata file"), + make_option(c("-n", "--names"), action = "store", default = NA, type = "character", + help = "Specific sample names"), + make_option(c("--plotmeta"), action = "store", default = NULL, type = "character", + help = "Plots counts per cell or genes per cell"), + make_option(c("--samples"), action = "store", default = NULL, type = "character", + help = "Samples to include in plots, defaults to all"), + make_option(c("--sminreads"), action = "store", default = 0, type = "integer", + help = "Minimum number of total reads for a spot to be retained"), + make_option(c("--smaxreads"), action = "store", default = NULL, type = "integer", + help = "Maximum number of total reads for a spot to be retained"), + make_option(c("--smingenes"), action = "store", default = 0, type = "integer", + help = "Minimum number of non-zero counts for a spot to be retained"), + make_option(c("--smaxgenes"), action = "store", default = NULL, type = "integer", + help = "Maximum number of non-zero counts for a spot to be retained"), + make_option(c("--gminreads"), action = "store", default = 0, type = "integer", + help = "Minimum number of total reads for a gene to be retained"), + make_option(c("--gmaxreads"), action = "store", default = NULL, type = "integer", + help = "Maximum number of total reads for a gene to be retained"), + make_option(c("--gminspots"), action = "store", default = 0, type = "integer", + help = "Minimum number of spots with non-zero counts for a gene to be retained"), + make_option(c("--gmaxspots"), action = "store", default = NULL, type = "integer", + help = "Maximum number of spots with non-zero counts for a gene to be retained"), + make_option(c("--distplot"), action = "store_true", type = "logical", default = FALSE, + help = "If set, generate unfiltered distribution plot"), + make_option(c("--filter"), action = "store_true", type = "logical", default = FALSE, + help = "If set, apply filtering before transformation"), + make_option(c("--filterplot"), action = "store_true", type = "logical", default = FALSE, + help = "If set, generate filtered distribution plot"), + make_option(c("-t", "--type"), action = "store_true", default = "log", type = "character", + help = "Type of transformation to apply: log or sct") +) + +### Main + +#parse args +opt <- parse_args(OptionParser(option_list = option_list)) + +#check if metadata or sample names were provided +#need metadata for raw and visium data, sample names for cosmx +if (!is.na(opt$meta) && is.na(opt$names)) { + samples_input <- opt$meta +} else if (is.na(opt$meta) && !is.na(opt$names)) { + samples_input <- unlist(strsplit(opt$names, split = ",")) +} else { + stop("Please only specify either --metadata OR --names") +} + +#create temporary directory to hold count data +count_dir <- tempdir() +unlink(count_dir, recursive = TRUE) +dir.create(count_dir) + +#create temporary directory to hold coord data +coord_dir <- tempdir() +unlink(coord_dir, recursive = TRUE) +dir.create(coord_dir) + +#if spotcoords were provided, load in count and coord data +#if spotcoords were not provided (visium input), only load the count file +if (!is.null(opt$spots)) { + coord_dir <- as.character(opt$spots) + coord_file <- fs::dir_ls(coord_dir) + count_dir <- as.character(opt$counts) + count_file <- fs::dir_ls(count_dir) +} else { + count_dir <- as.character(opt$counts) + count_file <- fs::dir_ls(count_dir) +} + +#if spotcoords are present, include in stlist input +if (!is.null(opt$spots)) { + st_data <- STlist(rnacounts = count_file, spotcoords = coord_file, samples = samples_input) +} else { + st_data <- STlist(rnacounts = count_file, samples = samples_input) +} + +message("STList has been created") + +#distribution plot + +#create distribution plot if flag is included +if (opt$distplot) { + + #if sample names are provided, separate the character string + if (!is.null(opt$samples) && opt$samples != "") { + sample_names <- strsplit(opt$samples, split = ",", fixed = TRUE)[[1]] + } else { + sample_names <- NULL + } + + #generate distribution plot + dist_plot <- distribution_plots(x = st_data, plot_meta = opt$plotmeta, samples = sample_names, ptsize = 1) + + #create unique plot file names based on sample name + base_input <- basename(opt$counts) + base_name <- file_path_sans_ext(base_input) + + filename <- paste0("unfiltered_", base_name, ".png") + + #create output directory for distribution plots + dir.create("./unfiltered_distribution_plots", showWarnings = FALSE, recursive = TRUE) + + #save plot to subdir + ggsave( + path = "./unfiltered_distribution_plots", + filename = filename, + bg = "white", + width = 12 + ) + + message("Unfiltered distribution plot saved to ./unfiltered_distribution_plots") +} + +#spot/cell filtering + +#filter spots if flag is included +if (opt$filter) { + + #filter out spots or genes based on minimum and maximum counts + st_data <- filter_data(x = st_data, spot_minreads = opt$sminreads, spot_maxreads = opt$smaxreads, spot_mingenes = opt$smingenes, + spot_maxgenes = opt$smaxgenes, gene_minreads = opt$gminreads) + message("Data filtering completed & saved to STlist") +} + +#filtered data plot + +#create filtered distribution plot if flag is included +if (opt$filterplot) { + + #if sample names are provided, separate the character string + if (!is.null(opt$samples) && opt$samples != "") { + sample_names <- strsplit(opt$samples, split = ",", fixed = TRUE)[[1]] + } else { + sample_names <- NULL + } + + #generate filtered distribution plot + filter_dist_plot <- distribution_plots(x = st_data, plot_meta = opt$plotmeta, samples = sample_names, ptsize = 1) + + #create unique plot file names based on sample name + base_input_2 <- basename(opt$counts) + base_name_2 <- file_path_sans_ext(base_input_2) + + filename_2 <- paste0("filtered_", base_name_2, ".png") + + #create output directory for cluster plots + dir.create("./filtered_distribution_plots", showWarnings = FALSE, recursive = TRUE) + + #save plot to subdir + ggsave( + path = "./filtered_distribution_plots", + filename = filename_2, + bg = "white", + width = 12 + ) + + message("Filtered distribution plot saved to ./filtered_distribution_plots") +} + +#transform data, defaults to log transformation + +STobj <- transform_data(x = st_data, method = opt$type) + +message("Data has been log transformed, unless otherwise specified") + +#save transformed data to .rds + +saveRDS(STobj, file = "STobj.rds") + +message("STlist has been saved as .rds file")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spatialGE_single_input.R Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,174 @@ +# ------------- +# Data Cleaning +# ------------- + +# SINGLE INPUT SCRIPT: +# Accepts single raw data sample and single cosmx sample +# Does not accept single visium sample due to spatial subdirectory + +# Purpose: +# Transform data into STlist, perform QC, log transform + +library(spatialGE) +library(optparse) +library(ggplot2) +library(tools) +library(fs) + + +### Command line options + +option_list <- list( + make_option(c("-c", "--counts"), action = "store", default = NA, type = "character", + help = "Path to count data file(s)"), + make_option(c("-s", "--spots"), action = "store", default = NULL, type = "character", + help = "Path to cell coordinates file(s), not required for Visium or Xenium"), + make_option(c("-m", "--meta"), action = "store", default = NA, type = "character", + help = "Path to metadata file"), + make_option(c("-n", "--names"), action = "store", default = NA, type = "character", + help = "Specific sample names"), + make_option(c("--plotmeta"), action = "store", default = NULL, type = "character", + help = "Plots counts per cell or genes per cell"), + make_option(c("--samples"), action = "store", default = NULL, type = "character", + help = "Samples to include in plots, defaults to all"), + make_option(c("--sminreads"), action = "store", default = 0, type = "integer", + help = "Minimum number of total reads for a spot to be retained"), + make_option(c("--smaxreads"), action = "store", default = NULL, type = "integer", + help = "Maximum number of total reads for a spot to be retained"), + make_option(c("--smingenes"), action = "store", default = 0, type = "integer", + help = "Minimum number of non-zero counts for a spot to be retained"), + make_option(c("--smaxgenes"), action = "store", default = NULL, type = "integer", + help = "Maximum number of non-zero counts for a spot to be retained"), + make_option(c("--gminreads"), action = "store", default = 0, type = "integer", + help = "Minimum number of total reads for a gene to be retained"), + make_option(c("--gmaxreads"), action = "store", default = NULL, type = "integer", + help = "Maximum number of total reads for a gene to be retained"), + make_option(c("--gminspots"), action = "store", default = 0, type = "integer", + help = "Minimum number of spots with non-zero counts for a gene to be retained"), + make_option(c("--gmaxspots"), action = "store", default = NULL, type = "integer", + help = "Maximum number of spots with non-zero counts for a gene to be retained"), + make_option(c("--distplot"), action = "store_true", type = "logical", default = FALSE, + help = "If set, generate unfiltered distribution plot"), + make_option(c("--filter"), action = "store_true", type = "logical", default = FALSE, + help = "If set, apply filtering before transformation"), + make_option(c("--filterplot"), action = "store_true", type = "logical", default = FALSE, + help = "If set, generate filtered distribution plot"), + make_option(c("-t", "--type"), action = "store_true", default = "log", type = "character", + help = "Type of transformation to apply: log or sct") +) + +### Main + +#parse args +opt <- parse_args(OptionParser(option_list = option_list)) + +#check if metadata or sample names were provided +#need metadata for raw, sample names for cosmx +if (!is.na(opt$meta) && is.na(opt$names)) { + samples_input <- opt$meta +} else if (is.na(opt$meta) && !is.na(opt$names)) { + samples_input <- opt$names +} else { + stop("Please only specify either --metadata OR --names") +} + +#create STlist with single input flags +st_data <- STlist(rnacounts = opt$counts, spotcoords = opt$spots, samples = samples_input) + +message("STlist has been created") + +#distribution plot + +#create distribution plot if flag is included +if (opt$distplot) { + + #if sample names are provided, separate the character string + #probably don't need strsplit, keeping for safety + if (!is.null(opt$samples) && opt$samples != "") { + sample_names <- strsplit(opt$samples, split = ",", fixed = TRUE)[[1]] + } else { + sample_names <- NULL + } + + #generate distribution plot + dist_plot <- distribution_plots(x = st_data, plot_meta = opt$plotmeta, samples = sample_names, ptsize = 1) + + #create unique plot file names based on sample name + base_input <- basename(opt$counts) + base_name <- file_path_sans_ext(base_input) + + filename <- paste0("unfiltered_", base_name, ".png") + + #create output directory for cluster plots + dir.create("./unfiltered_distribution_plots", showWarnings = FALSE, recursive = TRUE) + + #save plot to subdir + ggsave( + path = "./unfiltered_distribution_plots", + filename = filename, + bg = "white", + width = 12 + ) + + message("Unfiltered distribution plot saved to ./unfiltered_distribution_plots") +} + +#spot/cell filtering + +#filter spots if flag is included +if (opt$filter) { + + #filter out spots or genes based on minimum and maximum counts + st_data <- filter_data(x = st_data, spot_minreads = opt$sminreads, spot_maxreads = opt$smaxreads, spot_mingenes = opt$smingenes, + spot_maxgenes = opt$smaxgenes, gene_minreads = opt$gminreads) + + message("Data filtering completed & saved to STlist") +} + +#filtered data plot + +#create filtered distribution plot if flag is included +if (opt$filterplot) { + + #if sample names are provided, separate the character string + #probably don't need strsplit, keeping for safety + if (!is.null(opt$samples) && opt$samples != "") { + sample_names <- strsplit(opt$samples, split = ",", fixed = TRUE)[[1]] + } else { + sample_names <- NULL + } + + #generate filtered distribution plot + filter_dist_plot <- distribution_plots(x = st_data, plot_meta = opt$plotmeta, samples = sample_names, ptsize = 1) + + #create unique plot file names based on sample name + base_input_2 <- basename(opt$counts) + base_name_2 <- file_path_sans_ext(base_input_2) + + filename_2 <- paste0("filtered_", base_name_2, ".png") + + #create output directory for cluster plots + dir.create("./filtered_distribution_plots", showWarnings = FALSE, recursive = TRUE) + + #save plot to subdir + ggsave( + path = "./filtered_distribution_plots", + filename = filename_2, + bg = "white", + width = 12 + ) + + message("Filtered distribution plot saved to ./filtered_distribution_plots") +} + +#transform data, defaults to log transformation + +STobj <- transform_data(x = st_data, method = opt$type) + +message("Data has been log transformed, unless otherwise specified") + +#save transformed data to .rds + +saveRDS(STobj, file = "STobj.rds") + +message("STlist has been saved as .rds file")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ST_mel3_rep1_counts.tsv Wed Aug 13 19:32:19 2025 +0000 @@ -0,0 +1,1000 @@ +gene 5x8 6x8 6x9 6x10 7x7 7x8 7x9 7x10 7x11 7x12 8x7 8x8 8x9 8x10 8x11 8x12 8x13 8x14 9x6 9x7 9x8 9x9 9x10 9x11 9x12 9x13 9x14 9x15 9x16 9x17 10x6 10x7 10x8 10x9 10x10 10x11 10x12 10x13 10x15 10x16 10x17 10x18 10x19 11x6 11x7 11x8 11x9 11x10 11x11 11x12 11x13 11x14 11x15 11x16 11x17 11x18 11x19 11x20 12x6 12x7 12x8 12x9 12x10 12x11 12x12 12x13 12x14 12x15 12x16 12x17 12x18 12x19 12x20 12x21 12x22 12x23 12x24 13x6 13x7 13x8 13x9 13x10 13x11 13x12 13x13 13x14 13x15 13x16 13x17 13x18 13x19 13x20 13x21 13x22 13x23 13x24 13x25 13x26 13x27 14x6 14x7 14x8 14x9 14x10 14x11 14x12 14x13 14x14 14x15 14x16 14x17 14x18 14x19 14x20 14x21 14x22 14x23 14x24 14x25 14x26 14x27 15x6 15x7 15x8 15x9 15x10 15x11 15x12 15x13 15x14 15x15 15x16 15x17 15x18 15x19 15x20 15x21 15x23 15x24 15x25 15x26 15x27 16x6 16x7 16x8 16x9 16x10 16x11 16x12 16x13 16x14 16x15 16x16 16x17 16x18 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