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Seurat 4 + seurat convert + mappings tools (#251)
* Seurat convert passing 4/5 tests - no data uploaded yet * Passing AnnData reading test * Ready for trying tests locally * Passing all Seurat tests with planemo locally * Profile and version history * Almost all tests passing with Seurat 4 * All seurat 4 tests passing locally * Seurat UMAP passing test and macro mapper * Seurat AnnData Scanpy 1.8.2 test data retrieval and test hidden * Point to nature methods paper (cherry picked from commit 1ea601d) * Seurat integration and macro WIP * fix loom and others multi-inputs * Seurat integration test data, integration passing lints and tests, tags for umap * Remove repeated options * Seurat map query (all done last night) * Select integration features passing planemo tests * Integration passing tests after adding file option for int. features * Seurat plot * Plot linting passes, initial testing, fixes * Working plots on UI with adequate namings * Seurat plot passing planemo test locally * DoHeatmap with tests * Hover locator * Sanitise potential injections * Please linter warning * History and lintern pleasing * Remove AnnData as input and make sure it is as output * Documentation * Fix version in macro * AnnData is a valid input * Seurat dimplot test expected size * Seurat plot test sizes fixes * Fix plottting labels for linting * Fix input files for seurat_map * Try with conditional nesting for linting * Fix test data downloads * Change map-query missing input * Scale data multipe regress out vars * Map query refdata param changes * Fix scale data vars to regress * Use EBI OC query link for classify query * Size comparison for seurat map query
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tools/tertiary-analysis/seurat/extra/macro_mapper_seurat.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| --- | ||
| - option_group: | ||
| - input-object-file | ||
| - input-format | ||
| pre_command_macros: | ||
| - INPUT_OBJ_PREAMBLE | ||
| post_command_macros: | ||
| - INPUT_OBJECT | ||
| input_declaration_macros: | ||
| - input_object_params | ||
| - option_group: | ||
| - output-object-file | ||
| - output-format | ||
| post_command_macros: | ||
| - OUTPUT_OBJECT | ||
| input_declaration_macros: | ||
| - output_object_params | ||
| output_declaration_macros: | ||
| - output_files | ||
| - option_group: | ||
| - input-object-files | ||
| - input-format | ||
| pre_command_macros: | ||
| - INPUT_OBJS_PREAMBLE | ||
| post_command_macros: | ||
| - INPUT_OBJECTS | ||
| input_declaration_macros: | ||
| - input_object_params: | ||
| multiple: true | ||
| - option_group: | ||
| - reference-object-files | ||
| - reference-format | ||
| pre_command_macros: | ||
| - REFERENCE_OBJS_PREAMBLE | ||
| post_command_macros: | ||
| - REFERENCE_OBJECTS | ||
| input_declaration_macros: | ||
| - input_object_params: | ||
| varname: reference | ||
| multiple: true | ||
| optional: true | ||
| - option_group: | ||
| - reference-object-file | ||
| - reference-format | ||
| pre_command_macros: | ||
| - REFERENCE_OBJ_PREAMBLE | ||
| post_command_macros: | ||
| - REFERENCE_OBJECT | ||
| input_declaration_macros: | ||
| - input_object_params: | ||
| varname: reference | ||
| - option_group: | ||
| - anchors-object-file | ||
| - anchors-format | ||
| pre_command_macros: | ||
| - ANCHORS_OBJ_PREAMBLE | ||
| post_command_macros: | ||
| - ANCHORS_OBJECT | ||
| input_declaration_macros: | ||
| - input_object_params: | ||
| varname: anchors | ||
| - option_group: | ||
| - query-object-file | ||
| - query-format | ||
| pre_command_macros: | ||
| - QUERY_OBJ_PREAMBLE | ||
| post_command_macros: | ||
| - QUERY_OBJECT | ||
| input_declaration_macros: | ||
| - input_object_params: | ||
| varname: query | ||
| - option_group: | ||
| - plot-out | ||
| post_command_macros: | ||
| - OUTPUT_PLOT | ||
| output_declaration_macros: | ||
| - plot_output_files_format: | ||
| format: png | ||
| - plot_output_files_format: | ||
| format: pdf | ||
| - plot_output_files_format: | ||
| format: eps | ||
| - plot_output_files_format: | ||
| format: jpg | ||
| - plot_output_files_format: | ||
| format: ps | ||
| - plot_output_files_format: | ||
| format: tiff | ||
| - plot_output_files_format: | ||
| format: svg |
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165 changes: 165 additions & 0 deletions
165
tools/tertiary-analysis/seurat/scripts/seurat-scale-data.R
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,165 @@ | ||
| #!/usr/bin/env Rscript | ||
|
|
||
| # Load optparse we need to check inputs | ||
|
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||
| suppressPackageStartupMessages(require(optparse)) | ||
|
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| # Load common functions | ||
|
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| suppressPackageStartupMessages(require(workflowscriptscommon)) | ||
|
|
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| # parse options | ||
|
|
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| option_list = list( | ||
| make_option( | ||
| c("-i", "--input-object-file"), | ||
| action = "store", | ||
| default = NA, | ||
| type = 'character', | ||
| help = "File name in which a serialized R matrix object may be found." | ||
| ), | ||
| make_option( | ||
| c("--input-format"), | ||
| action = "store", | ||
| default = "seurat", | ||
| type = 'character', | ||
| help = "Either loom, seurat, anndata or singlecellexperiment for the input format to read." | ||
| ), | ||
| make_option( | ||
| c("--output-format"), | ||
| action = "store", | ||
| default = "seurat", | ||
| type = 'character', | ||
| help = "Either loom, seurat, anndata or singlecellexperiment for the output format." | ||
| ), | ||
| make_option( | ||
| c("-e", "--genes-use"), | ||
| action = "store", | ||
| default = NULL, | ||
| type = 'character', | ||
| help = "File with gene names to scale/center (one gene per line). Default is all genes in object@data." | ||
| ), | ||
| make_option( | ||
| c("-v", "--vars-to-regress"), | ||
| action = "store", | ||
| default = NULL, | ||
| type = 'character', | ||
| help = "Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito." | ||
| ), | ||
| make_option( | ||
| c("-m", "--model-use"), | ||
| action = "store", | ||
| default = 'linear', | ||
| type = 'character', | ||
| help = "Use a linear model or generalized linear model (poisson, negative binomial) for the regression. Options are 'linear' (default), 'poisson', and 'negbinom'." | ||
| ), | ||
| make_option( | ||
| c("-u", "--use-umi"), | ||
| action = "store", | ||
| default = FALSE, | ||
| type = 'logical', | ||
| help = "Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'." | ||
| ), | ||
| make_option( | ||
| c("-s", "--do-not-scale"), | ||
| action = "store_true", | ||
| default = FALSE, | ||
| type = 'logical', | ||
| help = "Skip the data scale." | ||
| ), | ||
| make_option( | ||
| c("-c", "--do-not-center"), | ||
| action = "store_true", | ||
| default = FALSE, | ||
| type = 'logical', | ||
| help = "Skip data centering." | ||
| ), | ||
| make_option( | ||
| c("-x", "--scale-max"), | ||
| action = "store", | ||
| default = 10, | ||
| type = 'double', | ||
| help = "Max value to return for scaled data. The default is 10. Setting this can help reduce the effects of genes that are only expressed in a very small number of cells. If regressing out latent variables and using a non-linear model, the default is 50." | ||
| ), | ||
| make_option( | ||
| c("-b", "--block-size"), | ||
| action = "store", | ||
| default = 1000, | ||
| type = 'integer', | ||
| help = "Default size for number of genes to scale at in a single computation. Increasing block.size may speed up calculations but at an additional memory cost." | ||
| ), | ||
| make_option( | ||
| c("-d", "--min-cells-to-block"), | ||
| action = "store", | ||
| default = 1000, | ||
| type = 'integer', | ||
| help = "If object contains fewer than this number of cells, don't block for scaling calculations." | ||
| ), | ||
| make_option( | ||
| c("-n", "--check-for-norm"), | ||
| action = "store", | ||
| default = TRUE, | ||
| type = 'logical', | ||
| help = "Check to see if data has been normalized, if not, output a warning (TRUE by default)." | ||
| ), | ||
| make_option( | ||
| c("-o", "--output-object-file"), | ||
| action = "store", | ||
| default = NA, | ||
| type = 'character', | ||
| help = "File name in which to store serialized R object of type 'Seurat'.'" | ||
| ) | ||
| ) | ||
|
|
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| opt <- wsc_parse_args(option_list, mandatory = c('input_object_file', 'output_object_file')) | ||
|
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| # Check parameter values | ||
|
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| if ( ! file.exists(opt$input_object_file)){ | ||
| stop((paste('File', opt$input_object_file, 'does not exist'))) | ||
| } | ||
|
|
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| if (! is.null(opt$genes_use)){ | ||
| if (! file.exists(opt$genes_use)){ | ||
| stop((paste('Supplied genes file', opt$genes_use, 'does not exist'))) | ||
| }else{ | ||
| genes_use <- readLines(opt$genes_use) | ||
| } | ||
| }else{ | ||
| genes_use <- NULL | ||
| } | ||
|
|
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| # break up opt$vars_to_regress into a list if it has commas | ||
| opt$vars_to_regress <- unlist(strsplit(opt$vars_to_regress, ",")) | ||
|
|
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| # Now we're hapy with the arguments, load Seurat and do the work | ||
|
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| suppressPackageStartupMessages(require(Seurat)) | ||
| if(opt$input_format == "loom" | opt$output_format == "loom") { | ||
| suppressPackageStartupMessages(require(SeuratDisk)) | ||
| } else if(opt$input_format == "singlecellexperiment" | opt$output_format == "singlecellexperiment") { | ||
| suppressPackageStartupMessages(require(scater)) | ||
| } | ||
|
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| # Input from serialized R object | ||
|
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| seurat_object <- read_seurat4_object(input_path = opt$input_object_file, format = opt$input_format) | ||
| # https://stackoverflow.com/questions/9129673/passing-list-of-named-parameters-to-function | ||
| # might be useful | ||
| scaled_seurat_object <- ScaleData(seurat_object, | ||
| features = genes_use, | ||
| vars.to.regress = opt$vars_to_regress, | ||
| model.use = opt$model_use, | ||
| use.umi = opt$use_umi, | ||
| do.scale = !opt$do_not_scale, | ||
| do.center = !opt$do_not_center, | ||
| scale.max = opt$scale_max, | ||
| block.size = opt$block_size, | ||
| min.cells.to.block = opt$min_cells_to_block, | ||
| verbose = FALSE) | ||
|
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|
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| # Output to a serialized R object | ||
| write_seurat4_object(seurat_object = scaled_seurat_object, | ||
| output_path = opt$output_object_file, | ||
| format = opt$output_format) |
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