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t-SNE_S1_cluster.R
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t-SNE_S1_cluster.R
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set.seed(42)
.libPaths('/lustre1/lch3000_pkuhpc/liuyf/R/R-3.4.1/library')
library(viridis)
library(monocle)
load('/lustre1/lch3000_pkuhpc/liuyf/denglab/zhaoting/monocle/AGG_estimate_size_and_dispersion.Robj')
Batch_vec <- c('MEF', 'SI5D', 'SI12D', 'XEN', 'SII8D', 'SII12D', 'SIII3D', 'SIII6D', 'SIII8D', 'SIII10D', 'SIII15D', 'SIII21D')
Batch_cols <- viridis(12, option = 'viridis')
names(Batch_cols) <- Batch_vec
Batch_labels <- c('MEF', 'SI D5', 'SI D12', 'XEN', 'SII D8', 'SII D12', 'SIII D3', 'SIII D6', 'SIII D8', 'SIII D10', 'SIII D15', 'SIII D21')
orderingGenes <- c("ENSMUSG00000028773","ENSMUSG00000038676","ENSMUSG00000008540","ENSMUSG00000061232","ENSMUSG00000020029","ENSMUSG00000026421","ENSMUSG00000018567","ENSMUSG00000054727","ENSMUSG00000056728","ENSMUSG00000001552","ENSMUSG00000005610","ENSMUSG00000050148","ENSMUSG00000020469","ENSMUSG00000027070","ENSMUSG00000038155","ENSMUSG00000075610","ENSMUSG00000018339","ENSMUSG00000028234","ENSMUSG00000029718","ENSMUSG00000027536","ENSMUSG00000060591","ENSMUSG00000014846","ENSMUSG00000038059","ENSMUSG00000034595","ENSMUSG00000038676","ENSMUSG00000049047","ENSMUSG00000044477","ENSMUSG00000030762","ENSMUSG00000044337","ENSMUSG00000000628","ENSMUSG00000033149","ENSMUSG00000032796","ENSMUSG00000029304","ENSMUSG00000029561","ENSMUSG00000095821","ENSMUSG00000054753","ENSMUSG00000022094","ENSMUSG00000023764","ENSMUSG00000021268","ENSMUSG00000026796","ENSMUSG00000081534","ENSMUSG00000005672","ENSMUSG00000059336","ENSMUSG00000086909","ENSMUSG00000059070","ENSMUSG00000061082","ENSMUSG00000003534","ENSMUSG00000001270","ENSMUSG00000029993","ENSMUSG00000022090","ENSMUSG00000032216","ENSMUSG00000019851","ENSMUSG00000018042","ENSMUSG00000030779","ENSMUSG00000031503","ENSMUSG00000032294","ENSMUSG00000045817","ENSMUSG00000027536","ENSMUSG00000046056","ENSMUSG00000020186","ENSMUSG00000029552","ENSMUSG00000032346","ENSMUSG00000014959","ENSMUSG00000022940","ENSMUSG00000040856","ENSMUSG00000001020","ENSMUSG00000026970","ENSMUSG00000028165","ENSMUSG00000099370","ENSMUSG00000005667","ENSMUSG00000032060","ENSMUSG00000027808","ENSMUSG00000106968","ENSMUSG00000024774","ENSMUSG00000027500","ENSMUSG00000001827","ENSMUSG00000023904","ENSMUSG00000032741","ENSMUSG00000023990","ENSMUSG00000091337","ENSMUSG00000038312","ENSMUSG00000022965","ENSMUSG00000062908","ENSMUSG00000028465","ENSMUSG00000061731","ENSMUSG00000039103","ENSMUSG00000031765","ENSMUSG00000031502","ENSMUSG00000035199","ENSMUSG00000029455","ENSMUSG00000018102","ENSMUSG00000054272","ENSMUSG00000022665","ENSMUSG00000024805","ENSMUSG00000022799","ENSMUSG00000056537","ENSMUSG00000067367","ENSMUSG00000049327","ENSMUSG00000021994","ENSMUSG00000029455","ENSMUSG00000008763","ENSMUSG00000028591","ENSMUSG00000053030","ENSMUSG00000003541","ENSMUSG00000047844","ENSMUSG00000027004","ENSMUSG00000041688","ENSMUSG00000042834","ENSMUSG00000063060","ENSMUSG00000029810","ENSMUSG00000015053","ENSMUSG00000030491","ENSMUSG00000078190","ENSMUSG00000057113","ENSMUSG00000027186","ENSMUSG00000028936","ENSMUSG00000023571","ENSMUSG00000032531","ENSMUSG00000038418","ENSMUSG00000035342","ENSMUSG00000033880","ENSMUSG00000025491","ENSMUSG00000037894","ENSMUSG00000022304","ENSMUSG00000030811","ENSMUSG00000067038","ENSMUSG00000033256","ENSMUSG00000092035","ENSMUSG00000042684","ENSMUSG00000091243","ENSMUSG00000049327","ENSMUSG00000061353","ENSMUSG00000028109","ENSMUSG00000006356","ENSMUSG00000031134","ENSMUSG00000053030","ENSMUSG00000021133","ENSMUSG00000035342","ENSMUSG00000026864","ENSMUSG00000032518","ENSMUSG00000026234","ENSMUSG00000006200","ENSMUSG00000027712","ENSMUSG00000022528","ENSMUSG00000027848","ENSMUSG00000046818","ENSMUSG00000034707","ENSMUSG00000034974","ENSMUSG00000035186","ENSMUSG00000029229","ENSMUSG00000023904","ENSMUSG00000042842","ENSMUSG00000064357","ENSMUSG00000023571","ENSMUSG00000059336","ENSMUSG00000030491","ENSMUSG00000085795","ENSMUSG00000028696","ENSMUSG00000019467","ENSMUSG00000024772","ENSMUSG00000020099","ENSMUSG00000018906","ENSMUSG00000023764","ENSMUSG00000100786","ENSMUSG00000023348","ENSMUSG00000079184","ENSMUSG00000063457","ENSMUSG00000023087","ENSMUSG00000038235","ENSMUSG00000058550","ENSMUSG00000039209","ENSMUSG00000028249","ENSMUSG00000027239","ENSMUSG00000029304","ENSMUSG00000044147","ENSMUSG00000037049","ENSMUSG00000032548","ENSMUSG00000097312","ENSMUSG00000025959","ENSMUSG00000028382","ENSMUSG00000021186","ENSMUSG00000006304","ENSMUSG00000061086","ENSMUSG00000050138","ENSMUSG00000022432","ENSMUSG00000027358","ENSMUSG00000019188","ENSMUSG00000032387","ENSMUSG00000001175","ENSMUSG00000078126","ENSMUSG00000048482","ENSMUSG00000032244","ENSMUSG00000032495","ENSMUSG00000034484","ENSMUSG00000029053","ENSMUSG00000057137","ENSMUSG00000019564","ENSMUSG00000050708","ENSMUSG00000028179","ENSMUSG00000021953","ENSMUSG00000038502","ENSMUSG00000033016","ENSMUSG00000021453","ENSMUSG00000037072","ENSMUSG00000036412","ENSMUSG00000020679","ENSMUSG00000025151","ENSMUSG00000001729","ENSMUSG00000027523","ENSMUSG00000019943","ENSMUSG00000067274","ENSMUSG00000044279","ENSMUSG00000021932","ENSMUSG00000039197","ENSMUSG00000039607","ENSMUSG00000027208","ENSMUSG00000000753","ENSMUSG00000056612","ENSMUSG00000025937","ENSMUSG00000027221","ENSMUSG00000010830","ENSMUSG00000007872","ENSMUSG00000055148","ENSMUSG00000032366","ENSMUSG00000095717","ENSMUSG00000006488","ENSMUSG00000030272","ENSMUSG00000050966","ENSMUSG00000052085","ENSMUSG00000046223","ENSMUSG00000032607","ENSMUSG00000020469","ENSMUSG00000025902","ENSMUSG00000015714","ENSMUSG00000026185","ENSMUSG00000001891","ENSMUSG00000074604","ENSMUSG00000030800",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AGG <- setOrderingFilter(AGG, orderingGenes)
png(file = paste0('t-SNE','_ordering','.png'), width = 7, height = 7, units = 'in', res = 300)
plot_ordering_genes(AGG)
dev.off()
png(file = paste0('t-SNE','_variance','.png'), width = 7, height = 7, units = 'in', res = 300)
plot_pc_variance_explained(AGG, return_all = T)
dev.off()
AGG <- reduceDimension(AGG, max_components = 2, norm_method = 'log', reduction_method = 'tSNE', num_dim = 10, verbose = T)
AGG <- clusterCells(AGG, verbose = T)
png(file = paste0('t-SNE','_cell_clusters_Batch','.png'), width = 7, height = 7, units = 'in', res = 300)
plot_cell_clusters(AGG, color_by = 'as.factor(Batch)', cell_size = 0.3) + scale_color_manual(labels = Batch_labels, values = Batch_cols, name = 'Batch')
dev.off()
png(file = paste0('t-SNE','_cell_clusters_Batch_facet','.png'), width = 7, height = 7, units = 'in', res = 300)
plot_cell_clusters(AGG, color_by = 'as.factor(Batch)', cell_size = 0.3) + facet_wrap(~Batch) + scale_color_manual(labels = Batch_labels, values = Batch_cols, name = 'Batch')
dev.off()
save(AGG, file = 't-SNE.Robj')
sessionInfo()