kandi X-RAY | seurat Summary
kandi X-RAY | seurat Summary
Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.
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seurat Examples and Code Snippets
Trending Discussions on seurat
I am creating ridge plots from the Seurat package. This packages utilizes ggplot2. All of my ridge plots look great except for one. I am trying to manually adjust the bandwidth to make this plot look similar to the others but I wind up with two ridge plots overlapping one another.
I can't post an example of the data as the data is a Seurat object and not a standard df. Apologies in advance!
Thank you for your help!
I have made good progress but I am still running into an issue. Ideally, ggplot2 would completely overwrite the previous points....
ANSWERAnswered 2022-Mar-23 at 14:50
I indirectly solved the issue I was having by changing the size of the bandwidth and the colors of the plots.
This code applies to a single plot.
p12 <- RidgePlot(sc1, features = "Y-27632") + geom_density_ridges2(scale = 4, bandwidth = 2.05) + theme(legend.position = "none") + xlab("Concentration [uM]") + ylab("Cluster") + scale_fill_manual( values = c("#FF3500A0", "#CC9933FF", "#33C04CCF", "#66CCFF", "#0000FF", "#FF66CC") )
I have build a singularity container based on r-base image and installing custom libraries like Seurat. Now I am trying to run my .Rmd script as follows:...
ANSWERAnswered 2022-Mar-21 at 11:50
$(...) statement is evaluated by bash and its output is what is sent to the singularity container. What you probably want is just:
I want to find
products and for each product attach
deals to it. A
deal is a
product from same collection, yet based on some common properties.
So as per my requirement pipeline should return documents, for each document find other products those aren't same as current, but have equal
detail.duration. But even though I've many docs with same duration,
deals are always
. Could you please figure out the issue with my pipeline?
Following is the aggregation pipeline I'm running: I've added filter _id $in just for clarity based on shown documents below. This isn't a part of real pipeline $match query....
ANSWERAnswered 2022-Feb-20 at 11:36
The $match query syntax is identical to the read operation query syntax; i.e. $match does not accept raw aggregation expressions. To include aggregation expression in $match, use a $expr query expression.
And you need to use
$$ to get the variable value.
To reference variables in pipeline stages, use the "$$" syntax.
$match stage in the pipeline as:
I am trying to update Rcpp from 1.0.6 to 1.0.7 or 1.0.8. The Rcpp update is essential for a primary R library that I intend to use.
I looked at the documentation and tried to install Rcpp using:...
ANSWERAnswered 2022-Feb-04 at 19:02
So you are using
Seurat. That is a big package with many recursive dependencies:
I'm trying to delete the first 7 characters of each string in a set of strings. I've been following akrun's wonderful answer here (how to add a character to a string in R). This is the command I've been using but it's returning an error:...
ANSWERAnswered 2022-Jan-02 at 08:34
You could use
substring, in combination with
paste0. If you want to replace each string individually, use
I've been trying to randomly subsample my seurat object. I'm interested in subsampling based on 2 columns: condition and cell type. I have 5 conditions and 5 cell types. Main goal is to have 1000 cells for each cell type in each condition. I've tried this so far:
First thing is subsetting my seurat object:...
ANSWERAnswered 2021-Nov-29 at 19:47
I can't say for certain without seeing your data, but could you just add an
if statement in the function? It looks like you're sampling column-wise, so check the number of columns. Just return x if the number of columns is less than the number you'd like to sample.
I was just wondering if anybody had any experience with coloring something like a UMAP made in ggplot based on the expression of multiple genes at the same time? What I want to do is something like the blend function in Seurat featureplots, but with 3 genes / colors instead of 2.
I'm looking to make something like this:
Where the colors for the genes combine where there is overlap.
What I've gotten to so far is...
ANSWERAnswered 2021-Oct-17 at 23:08
There is no 'vanilla' way of doing this in ggplot2. One can precalculate the blended colours and append invisible layers and scales with the ggnewscale package.
Let's pretend for reproducibility purposes that we want to make a UMAP of the iris dataset and using the descriptors of leaves as 'genes'.
I'm trying to subset a Seurat object (called dNSC_cells) based on counts of genes of interest. Specifically, I have a list of genes and I plan on looping through them to subset my data and do some Wilcox tests. What I have so far looks like this:...
ANSWERAnswered 2021-Sep-09 at 22:07
subset function does not support gene symbol in variable, you need to extract a dataframe first.
As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (https://ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it's probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA's tutorials (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/).
Here is what I have tried thus far:
This tries to replicate datExpr and datTraits from part I.1:...
ANSWERAnswered 2021-Aug-22 at 23:27
as.matrix(datExpr) right after
datExpr <- t(sobjwgcnamat)[,VariableFeatures(sobjwgcna)] worked. I had been trying it right before
MEList = moduleEigengenes(datExpr, colors = moduleColors)
and that didn't work. Seems simple but order matters I guess.
Currently I am trying to read a rds-file inside of a module. I am using the
golem package. This is my code right now and I don't know how to fix this.
Goal: Once the rds-file is uploaded the
conditionalPanel() should appear.
Problem: Reading the file failsCode
ANSWERAnswered 2021-Aug-09 at 14:28
The problem was with
readRDS(). I guess this is caused by the different
namespacing when working with modules.
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