Workshop Title
Authors: Josh Welch2.
Last modified: 17 July, 2020.
Description
LIGER analysis of scNMT-seq methylation and expression data from promoters, gene bodies, and putative enhancers
Promoter Methylation
library(liger)
#> Loading required package: cowplot
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#> Note: As of version 1.0.0, cowplot does not change the
#> default ggplot2 theme anymore. To recover the previous
#> behavior, execute:
#> theme_set(theme_cowplot())
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#> Loading required package: Matrix
#> Loading required package: patchwork
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#> Attaching package: 'patchwork'
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#> align_plots
library(MultiAssayExperiment)
#> Loading required package: SummarizedExperiment
#> Loading required package: GenomicRanges
#> Loading required package: stats4
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#> normalize
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gastru.mae <- readRDS(url('https://cloudstor.aarnet.edu.au/plus/s/Xzf5vCgAEUVgbfQ/download?path=%2Foutput&files=scnmtseq_gastrulation_mae_AllCells.rds'))
drop_lineages = c('Primitive_endoderm','Visceral_endoderm', 'ExE_ectoderm')
metadata = read.table("https://cloudstor.aarnet.edu.au/plus/s/Xzf5vCgAEUVgbfQ/download?path=%2Foutput&files=sample-metadata_matching-cells.txt",header=T,sep=",")
gastru.mae <- gastru.mae[,,grep("rna|met",names(assays(gastru.mae)))]
#> Loading required package: SingleCellExperiment
#> harmonizing input:
#> removing 4403 sampleMap rows not in names(experiments)
gastru.mae <- gastru.mae[, !(gastru.mae$lineage %in% drop_lineages),]
gastru.mae <- gastru.mae[,gastru.mae$pass_metQC==TRUE & gastru.mae$pass_rnaQC==TRUE]
proms <- experiments(gastru.mae)[["met_promoter"]]
genes <- experiments(gastru.mae)[["met_genebody"]]
rna <- counts(experiments(gastru.mae)[["rna"]])
proms[is.na(proms)] = 0
genes[is.na(genes)] = 0
all(colnames(proms)==colnames(rna))
#> [1] TRUE
colnames(proms)=paste0(colnames(proms),"_met")
colnames(genes)=paste0(colnames(genes),"_met")
rna_liger = createLiger(list(rna=rna,met=proms))
#> [1] "Removing 941 genes not expressing in rna."
rna_liger = liger::normalize(rna_liger)
rna_liger = liger::selectGenes(rna_liger,var.thresh = 1,datasets.use=1)
rna_liger = liger::scaleNotCenter(rna_liger)
rna_liger@norm.data[["met"]] = rna_liger@raw.data[["met"]] = as.matrix(100-proms)
rna_liger@var.genes = rna_liger@var.genes[rna_liger@var.genes %in% rownames(rna_liger@raw.data[["met"]])]
rna_liger@raw.data[["met"]] = Matrix(rna_liger@raw.data[["met"]],sparse=T)
rna_liger@norm.data[["met"]] = Matrix(rna_liger@norm.data[["met"]],sparse=T)
rna_liger@scale.data[["met"]] = t(as.matrix(rna_liger@norm.data[["met"]][rna_liger@var.genes,]))
rna_liger = optimizeALS(rna_liger,k=20)
#>
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#> Finished in 2.786395 mins, 30 iterations.
#> Max iterations set: 30.
#> Final objective delta: 0.0001333699.
#> Best results with seed 1.
rna_liger = quantile_norm(rna_liger)
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
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#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values
rna_liger = runTSNE(rna_liger)
metadata$id_met=paste0(metadata$id_met,"_met")
stage = c(as.character(metadata$stage),as.character(metadata$stage))
stage = as.factor(stage)
names(stage)=c(as.character(metadata$sample),as.character(metadata$id_met))
plotByDatasetAndCluster(rna_liger,clusters=stage,pt.size=1,text.size = 0)
#> Warning: Removed 1 rows containing missing values (geom_text).
Gene Body Methylation
rna_liger = createLiger(list(rna=rna,met=genes)) #> [1] "Removing 941 genes not expressing in rna." rna_liger = liger::normalize(rna_liger) rna_liger = liger::selectGenes(rna_liger,var.thresh = 1,datasets.use=1) rna_liger = liger::scaleNotCenter(rna_liger) rna_liger@norm.data[["met"]] = rna_liger@raw.data[["met"]] = genes rna_liger@var.genes = rna_liger@var.genes[rna_liger@var.genes %in% rownames(rna_liger@raw.data[["met"]])] rna_liger@raw.data[["met"]] = Matrix(rna_liger@raw.data[["met"]],sparse=T) rna_liger@norm.data[["met"]] = Matrix(rna_liger@norm.data[["met"]],sparse=T) rna_liger@scale.data[["met"]] = t(as.matrix(rna_liger@norm.data[["met"]][rna_liger@var.genes,])) rna_liger = optimizeALS(rna_liger,k=20) #> | | | 0% | |== | 3% | |===== | 7% | |======= | 10% | |========= | 13% | |============ | 17% | |============== | 20% | |================ | 23% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================== | 37% | |============================ | 40% | |============================== | 43% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================== | 57% | |========================================== | 60% | |============================================ | 63% | |=============================================== | 67% | |================================================= | 70% | |=================================================== | 73% | |====================================================== | 77% | |======================================================== | 80% | |========================================================== | 83% | |============================================================= | 87% | |=============================================================== | 90% | |================================================================= | 93% | |==================================================================== | 97% | |======================================================================| 100% #> Finished in 3.295458 mins, 30 iterations. #> Max iterations set: 30. #> Final objective delta: 8.118024e-05. #> Best results with seed 1. rna_liger = quantile_norm(rna_liger) #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values #> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): #> collapsing to unique 'x' values rna_liger = runTSNE(rna_liger) plotByDatasetAndCluster(rna_liger,clusters=stage,pt.size=1,text.size = 0)
#> Warning: Removed 1 rows containing missing values (geom_text).
University of Michigan↩︎