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Seurat Pipeline using the Seurat.utils package

License: GNU General Public License v3.0

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seurat.pipeline's Issues

Gene List plotting is buggy, needs a 'p$' style storage and cleanup.

Problem

Often breaks: if (TRUE) source('~/GitHub/Packages/Seurat.pipeline/elements/Gene.expression.gene.lists.R')
This is because GeneList variables are not defined
Without a list collection, they cant be auto-fetched.

Solution

Store genes in a master list in source('~/GitHub/Projects/AUT/GeneLists.AUT.R')
Store those in @misc
Recall ( Related to vertesy/Seurat.utils#20 )

AddGOGeneList.manual() used, but now only part of Gruffi's source code

Description
AddGOGeneList.manual() missing in if (TRUE) source('~/GitHub/Packages/Seurat.pipeline/elements/Differential.gene.expression.Loop.R'); create_set_Original_OutDir()

AddGOGeneList.manual <- function(obj = combined.obj, GO = 'GO:0034976'  # Add GO terms via Biomart package
                                 , genes =  c("A0A140VKG3", "ARX", "CNTN2", "DRD1", "DRD2", "FEZF2", "LHX6")) {
  genes <- IntersectWithExpressed(obj = obj, genes = genes)

  if (is.null(obj@misc$GO)) obj@misc$GO <- list()
  obj@misc$GO[[make.names(GO)]] <- genes
  iprint("Genes in", GO, "are saved under obj@misc$GO$", make.names(GO))
  if (web.open) system(paste0("open https://www.ebi.ac.uk/QuickGO/search/", GO))
  return(obj)
}

Needs clean up: `Gene.List.Overlap.R` and `Plot.gene.set.overlaps.R`

Both aim at the same goal, neither are complete.

Missing iteration index

Iteration index i missing in add.meta.fraction(..., obj = ls.Seurat[[1]]).

Seurat.Pipeline/00.Example.pipeline.for.sc.analysis.LOCAL.R

Line 49 in 9b33ec4

    
           ls.Seurat[[i]] <- add.meta.fraction(col.name = "percent.mito", gene.symbol.pattern = "^MT\\.|^MT-", obj = ls.Seurat[[1]])

Seurat.Pipeline/00.Example.pipeline.for.sc.analysis.LOCAL.R

Line 50 in 9b33ec4

    
           ls.Seurat[[i]] <- add.meta.fraction(col.name = "percent.ribo", gene.symbol.pattern = "^RPL|^RPS", obj = ls.Seurat[[1]])

How to analyze the data myself?

Where to find help?

Visualization by RStudio / Seurat

Link to What do you find in the single-cell analysis folder?

Overview of steps

Step	Command	Description
1	`install.packages()`	install packages
2	`require()`	load package
3	`readRDS()`	load Seurat object (sc data)
4	`recall.all.genes()`	create list of genes (all.genes
5	`all.genes$SATB2`	search for genes
6	`qUMAP()`	plot gene
7	`clUMAP()`	plot cluster

For the RenameGenes function in Seurat utils, how exactly does one manipulate the code to replace the dimnames with a new set of genes? I have a csv file containing the new names for all 28,444 genes in the original Seurat object, and would like to replace them with those names. In other words, what exactly does one change for "ls.Seurat" and "HGNC.updated.genes$Suggested.Symbol"? Thanks so much!

RenameGenesSeurat <- function(obj = ls.Seurat[[i]], newnames = HGNC.updated[[i]]$Suggested.Symbol) { # Replace gene names in different slots of a Seurat object. Run this before integration. Run this before integration. It only changes obj@assays$RNA@counts, @DaTa and @scale.data.
print("Run this before integration. It only changes obj@assays$RNA@counts, @DaTa and @scale.data.")
RNA <- obj@assays$RNA

if (nrow(RNA) == length(newnames)) {
if (length(RNA@counts)) RNA@counts@Dimnames[[1]] <- newnames
if (length(RNA@data)) RNA@data@Dimnames[[1]] <- newnames
if (length(RNA@scale.data)) RNA@scale.data@Dimnames[[1]] <- newnames
} else {"Unequal gene sets: nrow(RNA) != nrow(newnames)"}
obj@assays$RNA <- RNA
return(obj)
}
##RenameGenesSeurat(obj = SeuratObj, newnames = HGNC.updated.genes$Suggested.Symbol)

Error in STRING.db.auto.cluster.annotation.R

Description
A var seems like a df instead of a vector

if (TRUE) source("~/GitHub/Packages/Seurat.pipeline/elements/STRING.db.auto.cluster.annotation.R"); create_set_Original_OutDir()

error in

clnames.GO[cl.char] <-
    if (nrow(enrichmentGO)) {
      enrichmentGO$description[specific.GO.terms][1]
    } else {ppp('No Enrichment', i)} # if