seurat subset downsample
Why the obscure but specific description of Jane Doe II in the original complaint for Westenbroek v. Kappa Kappa Gamma Fraternity? Boolean algebra of the lattice of subspaces of a vector space? I have two seurat objects, one with about 40k cells and another with around 20k cells. Most functions now take an assay parameter, but you can set a Default Assay to avoid repetitive statements. Selecting cluster resolution using specificity criterion, Marker-based cell-type annotation using Miko Scoring, Gene program discovery using SSN analysis. Numeric [1,ncol(object)]. subset_deg <- function(obj . I dont have much choice, its either that or my R crashes with so many cells. How to refine signaling input into a handful of clusters out of many. With Seurat, you can easily switch between different assays at the single cell level (such as ADT counts from CITE-seq, or integrated/batch-corrected data). Thank you for the suggestion. Downsample each cell to a specified number of UMIs. Well occasionally send you account related emails. This can be misleading. What are the advantages of running a power tool on 240 V vs 120 V? between numbers are present in the feature name, Maximum number of cells per identity class, default is How to force Unity Editor/TestRunner to run at full speed when in background? Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. If the null hypothesis is never really true, is there a point to using a statistical test without a priori power analysis? What is the symbol (which looks similar to an equals sign) called? But this is something you can test by minimally subsetting your data (i.e. New blog post from our CEO Prashanth: Community is the future of AI, Improving the copy in the close modal and post notices - 2023 edition, Subsetting of object existing of two samples, Set new Idents based on gene expression in Seurat and mix n match identities to compare using FindAllMarkers, What column and row naming requirements exist with Seurat (context: when loading SPLiT-Seq data), Subsetting a Seurat object based on colnames, How to manage memory contraints when analyzing a large number of gene count matrices? downsample Maximum number of cells per identity class, default is Inf; downsampling will happen after all other operations, including inverting the cell selection seed Random seed for downsampling. 1 comment bari89 commented on Nov 18, 2021 mhkowalski closed this as completed on Nov 19, 2021 Sign up for free to join this conversation on GitHub . In other words - is there a way to randomly subscluster my cells in an unsupervised manner? Interpreting non-statistically significant results: Do we have "no evidence" or "insufficient evidence" to reject the null? invert, or downsample. 351 2 15. However, if you did not compute FindClusters() yet, all your cells would show the information stored in [email protected]$orig.ident in the object@ident slot. Well occasionally send you account related emails. the Allied commanders were appalled to learn that 300 glider troops had drowned at sea. Downsample a seurat object, either globally or subset by a field, The desired cell number to retain per unit of data. [: Simple subsetter for Seurat objects [ [: Metadata and associated object accessor dim (Seurat): Number of cells and features for the active assay dimnames (Seurat): The cell and feature names for the active assay head (Seurat): Get the first rows of cell-level metadata merge (Seurat): Merge two or more Seurat objects together to a point where your R doesn't crash, but that you loose the less cells), and then decreasing in the number of sampled cells and see if the results remain consistent and get recapitulated by lower number of cells. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Already on GitHub? You can subset from the counts matrix, below I use pbmc_small dataset from the package, and I get cells that are CD14+ and CD14-: library (Seurat) CD14_expression = GetAssayData (object = pbmc_small, assay = "RNA", slot = "data") ["CD14",] This vector contains the counts for CD14 and also the names of the cells: head (CD14_expression,30 . you may need to wrap feature names in backticks (``) if dashes If anybody happens upon this in the future, there was a missing ')' in the above code. Seurat has four tests for differential expression which can be set with the test.use parameter: ROC test ("roc"), t-test ("t"), LRT test based on zero-inflated data ("bimod", default), LRT test based on tobit-censoring models ("tobit") The ROC test returns the 'classification power' for any individual marker (ranging from 0 - random, to 1 - Great. Is a downhill scooter lighter than a downhill MTB with same performance? The final variable genes vector can be used for dimensional reduction. Numeric [0,1]. I am pretty new to Seurat. Seurat: Error in FetchData.Seurat(object = object, vars = unique(x = expr.char[vars.use]), : None of the requested variables were found: Ubiquitous regulation of highly specific marker genes. Yes it does randomly sample (using the sample() function from base). Subset of cell names. At the moment you are getting index from row comparison, then using that index to subset columns. inverting the cell selection, Random seed for downsampling. exp2 Astro 1000 cells. You can see the code that is actually called as such: SeuratObject:::subset.Seurat, which in turn calls SeuratObject:::WhichCells.Seurat (as @yuhanH mentioned). If you are going to use idents like that, make sure that you have told the software what your default ident category is. So if you clustered your cells (e.g. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. ctrl1 Astro 1000 cells You can set invert = TRUE, then it will exclude input cells. You signed in with another tab or window. identity class, high/low values for particular PCs, ect.. Otherwise, if you'd like to have equal number of cells (optimally) per cluster in your final dataset after subsetting, then what you proposed would do the job. Default is all identities. however, when i use subset(), it returns with Error. # Subset Seurat object based on identity class, also see ?SubsetData subset (x = pbmc, idents = "B cells") subset (x = pbmc, idents = c ("CD4 T cells", "CD8 T cells"), invert = TRUE) subset (x = pbmc, subset = MS4A1 > 3) subset (x = pbmc, subset = MS4A1 > 3 & PC1 > 5) subset (x = pbmc, subset = MS4A1 > 3, idents = "B cells") subset (x = pbmc, Number of cells to subsample. I think this is basically what you did, but I think this looks a little nicer. They actually both fail due to syntax errors, yours included @williamsdrake . Subset a Seurat object RDocumentation. Is there a way to maybe pick a set number of cells (but randomly) from the larger cluster so that I am comparing a similar number of cells? DoHeatmap ( subset (pbmc3k.final, downsample = 100), features = features, size = 3) New additions to FeaturePlot FeaturePlot (pbmc3k.final, features = "MS4A1") FeaturePlot (pbmc3k.final, features = "MS4A1", min.cutoff = 1, max.cutoff = 3) FeaturePlot (pbmc3k.final, features = c ("MS4A1", "PTPRCAP"), min.cutoff = "q10", max.cutoff = "q90") I would rather use the sample function directly. If the null hypothesis is never really true, is there a point to using a statistical test without a priori power analysis? Why does Acts not mention the deaths of Peter and Paul? Content Discovery initiative April 13 update: Related questions using a Review our technical responses for the 2023 Developer Survey, Filter data.frame rows by a logical condition, How to make a great R reproducible example, Subset data to contain only columns whose names match a condition. If this new subset is not randomly sampled, then on what criteria is it sampled? I checked the active.ident to make sure the identity has not shifted to any other column, but still I am getting the error? The number of column it is reduced ( so the object). The code could only make sense if the data is a square, equal number of rows and columns. The steps in the Seurat integration workflow are outlined in the figure below: Seurat (version 2.3.4) downsample: Maximum number of cells per identity class, default is Inf; downsampling will happen after all other operations, . I ma just worried it is just picking the first 600 and not randomizing, https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/sample. I appreciate the lively discussion and great suggestions - @leonfodoulian I used your method and was able to do exactly what I wanted. Here, the GEX = pbmc_small, for exemple. This subset also has the same exact mean and median as my original object Im subsetting from. For your last question, I suggest you read this bioRxiv paper. Image of minimal degree representation of quasisimple group unique up to conjugacy, Folder's list view has different sized fonts in different folders. to your account. There are 33 cells under the identity. as.Seurat: Coerce to a 'Seurat' Object; as.sparse: Cast to Sparse; AttachDeps: . Heatmap of gene subset from microarray expression data in R. How to filter genes from seuratobject in slotname @data? Try doing that, and see for yourself if the mean or the median remain the same. inplace: bool (default: True) If a subsetField is provided, the string 'min' can also be used, in which case, If provided, data will be grouped by these fields, and up to targetCells will be retained per group. Identity classes to subset. Thanks again for any help! SubsetData(object, cells.use = NULL, subset.name = NULL, ident.use = NULL, max.cells.per.ident. A stupid suggestion, but did you try to give it as a string ? subset.name = NULL, accept.low = -Inf, accept.high = Inf, Downsample Seurat Description. Two MacBook Pro with same model number (A1286) but different year. identity class, high/low values for particular PCs, etc. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What do hollow blue circles with a dot mean on the World Map? I have a seurat object with 5 conditions and 9 cell types defined. Thanks, downsample is an input parameter from WhichCells, Maximum number of cells per identity class, default is Inf; downsampling will happen after all other operations, including inverting the cell selection. Cell types: Micro, Astro, Oligo, Endo, InN, ExN, Pericyte, OPC, NasN, ctrl1 Micro 1000 cells Returns a list of cells that match a particular set of criteria such as identity class, high/low values for particular PCs, ect.. Learn R. Search all packages and functions. Again, Id like to confirm that it randomly samples! # install dataset InstallData ("ifnb") Therefore I wanted to confirm: does the SubsetData blindly randomly sample? Thanks for the answer! Already have an account? Have a question about this project? Returns a list of cells that match a particular set of criteria such as Hi Also, please provide a reproducible example data for testing, dput (myData). Making statements based on opinion; back them up with references or personal experience. privacy statement. Adding EV Charger (100A) in secondary panel (100A) fed off main (200A). Usage 1 2 3 Seurat (version 3.1.4) Description. This is due to having ~100k cells in my starting object so I randomly sampled 60k or 50k with the SubsetData as I mentioned to use for the downstream analysis. Making statements based on opinion; back them up with references or personal experience. The text was updated successfully, but these errors were encountered: I guess you can randomly sample your cells from that cluster using sample() (from the base in R). privacy statement. Why did US v. Assange skip the court of appeal? Learn R. Search all packages and functions. subset: bool (default: False) Inplace subset to highly-variable genes if True otherwise merely indicate highly variable genes. by default, throws an error, A predicate expression for feature/variable expression, I keep running out of RAM with my current pipeline, Bar Graph of Expression Data from Seurat Object. Examples Run this code # NOT . Can you tell me, when I use the downsample function, how does seurat exclude or choose cells? Using the same logic as @StupidWolf, I am getting the gene expression, then make a dataframe with two columns, and this information is directly added on the Seurat object. Downsample single cell data Downsample number of cells in Seurat object by specified factor downsampleSeurat( object , subsample.factor = 1 , subsample.n = NULL , sample.group = NULL , min.group.size = 500 , seed = 1023 , verbose = T ) Arguments Value Seurat Object Author Nicholas Mikolajewicz Related question: "SubsetData" cannot be directly used to randomly sample 1000 cells (let's say) from a larger object? data.table vs dplyr: can one do something well the other can't or does poorly? Sign in to comment Assignees No one assigned Labels None yet Projects None yet Milestone If anybody happens upon this in the future, there was a missing ')' in the above code. Indentity classes to remove. Example Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. You can check lines 714 to 716 in interaction.R. Any argument that can be retreived By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. By clicking Sign up for GitHub, you agree to our terms of service and Description Randomly subset (cells) seurat object by a rate Usage 1 RandomSubsetData (object, rate, random.subset.seed = NULL, .) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Well occasionally send you account related emails. To learn more, see our tips on writing great answers. Find centralized, trusted content and collaborate around the technologies you use most. Did the Golden Gate Bridge 'flatten' under the weight of 300,000 people in 1987? I followed the example in #243, however this issue used a previous version of Seurat and the code didn't work as-is. Learn more about Stack Overflow the company, and our products. Not the answer you're looking for? Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. Which language's style guidelines should be used when writing code that is supposed to be called from another language? If I verify the subsetted object, it does have the nr of cells I asked for in max.cells.per.ident (only one ident in one starting object). 4 comments chrismahony commented on May 19, 2020 Collaborator yuhanH closed this as completed on May 22, 2020 evanbiederstedt mentioned this issue on Dec 23, 2021 Downsample from each cluster kharchenkolab/conos#115 Connect and share knowledge within a single location that is structured and easy to search. What would be the best way to do it? For instance, you might do something like this: You signed in with another tab or window. Did the drapes in old theatres actually say "ASBESTOS" on them? Inf; downsampling will happen after all other operations, including Should I re-do this cinched PEX connection? This works for me, with the metadata column being called "group", and "endo" being one possible group there. Was Aristarchus the first to propose heliocentrism? For the new folks out there used to Satija lab vignettes, I'll just call large.obj pbmc, and downsampled.obj, pbmc.downsampled, and replace size determined by the number of columns in another object with an integer, 2999: I was trying to do the same and is used your code. 1. SampleUMI(data, max.umi = 1000, upsample = FALSE, verbose = FALSE) Arguments data Matrix with the raw count data max.umi Number of UMIs to sample to upsample Upsamples all cells with fewer than max.umi verbose How are engines numbered on Starship and Super Heavy? They actually both fail due to syntax errors, yours included @williamsdrake . These genes can then be used for dimensional reduction on the original data including all cells. Sign in Other option is to get the cell names of that ident and then pass a vector of cell names. Can be used to downsample the data to a certain max per cell ident. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Downsample number of cells in Seurat object by specified factor. My analysis is helped by the fact that the larger cluster is very homogeneous - so, random sampling of ~1000 cells is still very representative. If NULL, does not set a seed Value A vector of cell names See also FetchData Examples I would like to randomly downsample the larger object to have the same number of cells as the smaller object, however I am getting an error when trying to subset. privacy statement. Conditions: ctrl1, ctrl2, ctrl3, exp1, exp2 Analysis and visualization of Spatial Transcriptomics data, Search the jbergenstrahle/STUtility package, jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data. clusters or whichever idents are chosen), and then for each of those groups calls sample if it contains more than the requested number of cells. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. So, it's just a random selection. By clicking Sign up for GitHub, you agree to our terms of service and If ident.use = NULL, then Seurat looks at your actual object@ident (see Seurat::WhichCells, l.6). Cannot find cells provided, Any help or guidance would be appreciated. Have a question about this project? I want to create a subset of a cell expressing certain genes only. Identify blue/translucent jelly-like animal on beach. It only takes a minute to sign up. Appreciate the detailed code you wrote. However, for robustness issues, I would try to resample from obj1 several times using different seed values (which you can store for reproducibility), compute variable genes at each step as described above, and then get either the union or the intersection of those variable genes. What should I follow, if two altimeters show different altitudes? crash. Sign in Use MathJax to format equations. Creates a Seurat object containing only a subset of the cells in the original object. You can however change the seed value and end up with a different dataset. 1) The downsampled percentage of cells in WT and KO is more over same compared to the actual % of cells in WT and KO 2) In each versions, I have highlighted the KO cells for cluster 1, 4, 5, 6 and 7 where the downsampled number is less than the WT cells. You can then create a vector of cells including the sampled cells and the remaining cells, then subset your Seurat object using SubsetData() and compute the variable genes on this new Seurat object. The text was updated successfully, but these errors were encountered: This is more of a general R question than a question directly related to Seurat, but i will try to give you an idea. Downsample a seurat object, either globally or subset by a field Usage DownsampleSeurat(seuratObj, targetCells, subsetFields = NULL, seed = GetSeed()) Arguments. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. If you make a dataframe containing the barcodes, conditions, and celltypes, you can sample 1000 cells within each condition/ celltype. rev2023.5.1.43405. When do you use in the accusative case? Sign in Here is my coding but it always shows. privacy statement. The best answers are voted up and rise to the top, Not the answer you're looking for? For more information on customizing the embed code, read Embedding Snippets. Choose the flavor for identifying highly variable genes. How to subset the rows of my data frame based on a list of names? to your account. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Developed by Rahul Satija, Andrew Butler, Paul Hoffman, Tim Stuart. I can figure out what it is by doing the following: meta_data = colnames ([email protected]) [grepl ("DF.classification", colnames ([email protected]))] Where meta_data = 'DF.classifications_0.25_0.03_252' and is a character class. can evaluate anything that can be pulled by FetchData; please note, Numeric [1,ncol(object)]. RDocumentation. To use subset on a Seurat object, (see ?subset.Seurat) , you have to provide: What you have should work, but try calling the actual function (in case there are packages that clash): Thanks for contributing an answer to Bioinformatics Stack Exchange! Eg, the name of a gene, PC1, a To learn more, see our tips on writing great answers. Short story about swapping bodies as a job; the person who hires the main character misuses his body. You can then create a vector of cells including the sampled cells and the remaining cells, then subset your Seurat object using SubsetData() and compute the variable genes on this new Seurat object. However, to avoid cases where you might have different orig.ident stored in the [email protected] slot, which happened in my case, I suggest you create a new column where you have the same identity for all your cells, and set the identity of all your cells to that identity.
