约800个细胞
运行约1.5小时
限速步骤在18
> rm(list=ls())
> options(stringsAsFactors = F)
> library(Seurat)
> library(ggplot2)
> library(infercnv)
> expFile='expFile.txt'
> groupFiles='groupFiles.txt'
> geneFile='geneFile.txt'
> infercnv_obj = CreateInfercnvObject(raw_counts_matrix=expFile,
+ annotations_file=groupFiles,
+ delim="\t",
+ gene_order_file= geneFile,
+ ref_group_names=c('ref-fib')) ## 这个取决于自己的分组信息里面的
INFO [2021-03-11 15:50:23] Parsing matrix: expFile.txt
INFO [2021-03-11 15:50:26] Parsing gene order file: geneFile.txt
INFO [2021-03-11 15:50:26] Parsing cell annotations file: groupFiles.txt
INFO [2021-03-11 15:50:26] ::order_reduce:Start.
INFO [2021-03-11 15:50:26] .order_reduce(): expr and order match.
INFO [2021-03-11 15:50:26] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 12990,801 Total=6217810 Min=0 Max=1454.
INFO [2021-03-11 15:50:26] num genes removed taking into account provided gene ordering list: 440 = 3.38722093918399% removed.
INFO [2021-03-11 15:50:26] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2021-03-11 15:50:27] validating infercnv_obj
>
> ## 文献的代码：#14:58开始
> start_time <- Sys.time()
> infercnv_obj2 = infercnv::run(infercnv_obj,
+ cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
+ out_dir='plot_out2/' ,
+ cluster_by_groups=T, # cluster
+ hclust_method="ward.D2",
+ plot_steps=F,
+ denoise=T,
+ HMM=T)
INFO [2021-03-11 15:50:27] ::process_data:Start
INFO [2021-03-11 15:50:27] Creating output path plot_out2/
INFO [2021-03-11 15:50:27] Checking for saved results.
INFO [2021-03-11 15:50:27]
STEP 1: incoming data
INFO [2021-03-11 15:50:28]
STEP 02: Removing lowly expressed genes
INFO [2021-03-11 15:50:28] ::above_min_mean_expr_cutoff:Start
INFO [2021-03-11 15:50:28] Removing 8652 genes from matrix as below mean expr threshold: 0.1
INFO [2021-03-11 15:50:28] validating infercnv_obj
INFO [2021-03-11 15:50:28] There are 3898 genes and 801 cells remaining in the expr matrix.
INFO [2021-03-11 15:50:29] no genes removed due to min cells/gene filter
INFO [2021-03-11 15:50:30]
STEP 03: normalization by sequencing depth
INFO [2021-03-11 15:50:30] normalizing counts matrix by depth
INFO [2021-03-11 15:50:30] Computed total sum normalization factor as median libsize: 4616.000000
INFO [2021-03-11 15:50:30] Adding h-spike
INFO [2021-03-11 15:50:30] -hspike modeling of ref-fib
INFO [2021-03-11 15:51:22] validating infercnv_obj
INFO [2021-03-11 15:51:22] normalizing counts matrix by depth
INFO [2021-03-11 15:51:22] Using specified normalization factor: 4616.000000
INFO [2021-03-11 15:51:24]
STEP 04: log transformation of data
INFO [2021-03-11 15:51:24] transforming log2xplus1()
INFO [2021-03-11 15:51:24] -mirroring for hspike
INFO [2021-03-11 15:51:24] transforming log2xplus1()
INFO [2021-03-11 15:51:26]
STEP 08: removing average of reference data (before smoothing)
INFO [2021-03-11 15:51:26] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 15:51:26] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 15:51:28] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 15:51:28] -mirroring for hspike
INFO [2021-03-11 15:51:28] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 15:51:28] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 15:51:30] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 15:51:33]
STEP 09: apply max centered expression threshold: 3
INFO [2021-03-11 15:51:33] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 15:51:33] -mirroring for hspike
INFO [2021-03-11 15:51:33] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 15:51:35]
STEP 10: Smoothing data per cell by chromosome
INFO [2021-03-11 15:51:35] smooth_by_chromosome: chr: chr1
INFO [2021-03-11 15:51:36] smooth_by_chromosome: chr: chr10
INFO [2021-03-11 15:51:37] smooth_by_chromosome: chr: chr11
INFO [2021-03-11 15:51:38] smooth_by_chromosome: chr: chr12
INFO [2021-03-11 15:51:39] smooth_by_chromosome: chr: chr13
INFO [2021-03-11 15:51:39] smooth_by_chromosome: chr: chr14
INFO [2021-03-11 15:51:40] smooth_by_chromosome: chr: chr15
INFO [2021-03-11 15:51:41] smooth_by_chromosome: chr: chr16
INFO [2021-03-11 15:51:41] smooth_by_chromosome: chr: chr17
INFO [2021-03-11 15:51:42] smooth_by_chromosome: chr: chr18
INFO [2021-03-11 15:51:43] smooth_by_chromosome: chr: chr19
INFO [2021-03-11 15:51:44] smooth_by_chromosome: chr: chr2
INFO [2021-03-11 15:51:45] smooth_by_chromosome: chr: chr20
INFO [2021-03-11 15:51:45] smooth_by_chromosome: chr: chr21
INFO [2021-03-11 15:51:45] smooth_by_chromosome: chr: chr22
INFO [2021-03-11 15:51:46] smooth_by_chromosome: chr: chr3
INFO [2021-03-11 15:51:47] smooth_by_chromosome: chr: chr4
INFO [2021-03-11 15:51:48] smooth_by_chromosome: chr: chr5
INFO [2021-03-11 15:51:49] smooth_by_chromosome: chr: chr6
INFO [2021-03-11 15:51:49] smooth_by_chromosome: chr: chr7
INFO [2021-03-11 15:51:50] smooth_by_chromosome: chr: chr8
INFO [2021-03-11 15:51:51] smooth_by_chromosome: chr: chr9
INFO [2021-03-11 15:51:52] -mirroring for hspike
INFO [2021-03-11 15:51:52] smooth_by_chromosome: chr: chrA
INFO [2021-03-11 15:51:52] smooth_by_chromosome: chr: chr_0
INFO [2021-03-11 15:51:52] smooth_by_chromosome: chr: chr_B
INFO [2021-03-11 15:51:53] smooth_by_chromosome: chr: chr_0pt5
INFO [2021-03-11 15:51:53] smooth_by_chromosome: chr: chr_C
INFO [2021-03-11 15:51:53] smooth_by_chromosome: chr: chr_1pt5
INFO [2021-03-11 15:51:54] smooth_by_chromosome: chr: chr_D
INFO [2021-03-11 15:51:54] smooth_by_chromosome: chr: chr_2pt0
INFO [2021-03-11 15:51:55] smooth_by_chromosome: chr: chr_E
INFO [2021-03-11 15:51:55] smooth_by_chromosome: chr: chr_3pt0
INFO [2021-03-11 15:51:55] smooth_by_chromosome: chr: chr_F
INFO [2021-03-11 15:51:58]
STEP 11: re-centering data across chromosome after smoothing
INFO [2021-03-11 15:51:58] ::center_smooth across chromosomes per cell
INFO [2021-03-11 15:51:59] -mirroring for hspike
INFO [2021-03-11 15:51:59] ::center_smooth across chromosomes per cell
INFO [2021-03-11 15:52:02]
STEP 12: removing average of reference data (after smoothing)
INFO [2021-03-11 15:52:02] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 15:52:02] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 15:52:04] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 15:52:04] -mirroring for hspike
INFO [2021-03-11 15:52:04] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 15:52:04] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 15:52:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 15:52:09]
STEP 14: invert log2(FC) to FC
INFO [2021-03-11 15:52:09] invert_log2(), computing 2^x
INFO [2021-03-11 15:52:10] -mirroring for hspike
INFO [2021-03-11 15:52:10] invert_log2(), computing 2^x
INFO [2021-03-11 15:52:13]
STEP 15: Clustering samples (not defining tumor subclusters)
INFO [2021-03-11 15:52:13] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 15:52:13] define_signif_tumor_subclusters(), tumor: epi
INFO [2021-03-11 15:52:29] cut tree into: 1 groups
INFO [2021-03-11 15:52:29] -processing epi,epi_s1
INFO [2021-03-11 15:52:29] define_signif_tumor_subclusters(), tumor: ref-fib
INFO [2021-03-11 15:52:29] cut tree into: 1 groups
INFO [2021-03-11 15:52:29] -processing ref-fib,ref-fib_s1
INFO [2021-03-11 15:52:29] -mirroring for hspike
INFO [2021-03-11 15:52:29] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 15:52:29] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_ref-fib
INFO [2021-03-11 15:52:30] cut tree into: 1 groups
INFO [2021-03-11 15:52:30] -processing spike_tumor_cell_ref-fib,spike_tumor_cell_ref-fib_s1
INFO [2021-03-11 15:52:30] define_signif_tumor_subclusters(), tumor: simnorm_cell_ref-fib
INFO [2021-03-11 15:52:30] cut tree into: 1 groups
INFO [2021-03-11 15:52:30] -processing simnorm_cell_ref-fib,simnorm_cell_ref-fib_s1
INFO [2021-03-11 15:52:37] ::plot_cnv:Start
INFO [2021-03-11 15:52:37] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=3121713.45889506 Min=0.605612335994316 Max=1.59021417195841.
INFO [2021-03-11 15:52:37] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 15:52:46] plot_cnv(): auto thresholding at: (0.809977 , 1.189648)
INFO [2021-03-11 15:52:46] plot_cnv_observation:Start
INFO [2021-03-11 15:52:46] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 15:52:46] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 15:52:46] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 15:52:46] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 15:52:46] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 15:52:47] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 15:52:47] Quantiles of plotted data range: 0.809977199785157,0.951015034736446,0.997395922170644,1.04627646653569,1.18964837016048
INFO [2021-03-11 15:52:48] plot_cnv_observations:Writing observation data to plot_out2//infercnv.preliminary.observations.txt
INFO [2021-03-11 15:52:55] plot_cnv_references:Start
INFO [2021-03-11 15:52:55] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 15:52:56] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 15:52:56] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 15:52:56] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 15:52:56] Quantiles of plotted data range: 0.811707332091943,0.968235042208273,0.997405353126883,1.03026444546416,1.18964837016048
INFO [2021-03-11 15:52:56] plot_cnv_references:Writing reference data to plot_out2//infercnv.preliminary.references.txt
INFO [2021-03-11 15:52:58]
STEP 17: HMM-based CNV prediction
INFO [2021-03-11 15:52:58] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2021-03-11 15:53:00] -done predicting CNV based on initial tumor subclusters
INFO [2021-03-11 15:53:01] get_predicted_CNV_regions(subcluster)
INFO [2021-03-11 15:53:01] -processing cell_group_name: epi.epi_s1, size: 647
INFO [2021-03-11 15:53:09] -processing cell_group_name: ref-fib.ref-fib_s1, size: 154
INFO [2021-03-11 15:53:14] -writing cell clusters file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2021-03-11 15:53:14] -writing cnv regions file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2021-03-11 15:53:14] -writing per-gene cnv report: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2021-03-11 15:53:15] -writing gene ordering info: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2021-03-11 15:53:15] ::plot_cnv:Start
INFO [2021-03-11 15:53:15] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=9876730 Min=1 Max=6.
INFO [2021-03-11 15:53:15] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 15:53:21] plot_cnv_observation:Start
INFO [2021-03-11 15:53:21] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 15:53:21] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 15:53:21] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 15:53:21] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 15:53:21] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 15:53:22] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 15:53:22] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-11 15:53:23] plot_cnv_observations:Writing observation data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2021-03-11 15:53:28] plot_cnv_references:Start
INFO [2021-03-11 15:53:28] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 15:53:28] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 15:53:28] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 15:53:28] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 15:53:28] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-11 15:53:28] plot_cnv_references:Writing reference data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2021-03-11 15:53:30]
STEP 18: Run Bayesian Network Model on HMM predicted CNV's
INFO [2021-03-11 15:53:30] Creating the following Directory: plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2021-03-11 15:53:30] Initializing new MCM InferCNV Object.
INFO [2021-03-11 15:53:30] validating infercnv_obj
INFO [2021-03-11 15:53:30] Total CNV's: 52
INFO [2021-03-11 15:53:30] Loading BUGS Model.
INFO [2021-03-11 15:53:30] Running Sampling Using Parallel with 4 Cores
INFO [2021-03-11 17:27:22] Obtaining probabilities post-sampling
INFO [2021-03-11 17:31:37] Gibbs sampling time: 98.1105454325676 Minutes
INFO [2021-03-11 17:31:42] ::plot_cnv:Start
INFO [2021-03-11 17:31:42] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=1202349.77974189 Min=0 Max=0.99551055925607.
INFO [2021-03-11 17:31:42] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:31:43] plot_cnv_observation:Start
INFO [2021-03-11 17:31:43] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:31:43] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:31:43] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:31:43] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:31:43] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:31:43] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:31:43] Quantiles of plotted data range: 0,0,0.705438651918569,0.84818137456409,0.99551055925607
INFO [2021-03-11 17:31:44] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2021-03-11 17:31:52] plot_cnv_references:Start
INFO [2021-03-11 17:31:52] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:31:53] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:31:53] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:31:53] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:31:53] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-11 17:31:53] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2021-03-11 17:32:00] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2021-03-11 17:32:00] Removing 0 CNV(s) identified by the HMM.
INFO [2021-03-11 17:32:00] Reassigning CNVs based on state probabilities.
INFO [2021-03-11 17:32:00] Changing the following CNV's states assigned by the HMM to the following based on the CNV's state probabilities.
chr1-region_4 : 5 (P= 0.260671650811715 ) -> 4 (P= 0.369626566439322 )
chr14-region_27 : 4 (P= 0.323021003201177 ) -> 3 (P= 0.339918069890555 )
chr14-region_28 : 5 (P= 0.240193534973606 ) -> 4 (P= 0.313080165391468 )
chr16-region_32 : 5 (P= 0.325863484421546 ) -> 4 (P= 0.461231211008675 )
chr6-region_69 : 5 (P= 0.347602620065479 ) -> 4 (P= 0.464777989149583 )
chr7-region_74 : 4 (P= 0.362840364024948 ) -> 3 (P= 0.366104515821237 )
chr9-region_84 : 5 (P= 0.358420691011011 ) -> 4 (P= 0.387749927083735 )
INFO [2021-03-11 17:32:00] Creating Plots for CNV and cell Probabilities.
INFO [2021-03-11 17:33:14] ::plot_cnv:Start
INFO [2021-03-11 17:33:14] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=1202349.77974189 Min=0 Max=0.99551055925607.
INFO [2021-03-11 17:33:14] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:33:15] plot_cnv_observation:Start
INFO [2021-03-11 17:33:15] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:33:15] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:33:15] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:33:15] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:33:15] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:33:16] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:33:16] Quantiles of plotted data range: 0,0,0.705438651918569,0.84818137456409,0.99551055925607
INFO [2021-03-11 17:33:17] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.observations.txt
INFO [2021-03-11 17:33:27] plot_cnv_references:Start
INFO [2021-03-11 17:33:27] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:33:28] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:33:28] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:33:28] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:33:29] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-11 17:33:29] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.references.txt
INFO [2021-03-11 17:33:35] ::plot_cnv:Start
INFO [2021-03-11 17:33:35] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=9768034 Min=1 Max=6.
INFO [2021-03-11 17:33:35] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:33:49] plot_cnv_observation:Start
INFO [2021-03-11 17:33:49] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:33:49] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:33:49] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:33:49] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:33:49] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:33:50] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:33:50] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-11 17:33:51] plot_cnv_observations:Writing observation data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.observations.txt
INFO [2021-03-11 17:34:00] plot_cnv_references:Start
INFO [2021-03-11 17:34:00] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:34:01] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:34:01] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:34:01] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:34:01] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-11 17:34:01] plot_cnv_references:Writing reference data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.references.txt
INFO [2021-03-11 17:34:03]
STEP 19: Converting HMM-based CNV states to repr expr vals
INFO [2021-03-11 17:34:06] ::plot_cnv:Start
INFO [2021-03-11 17:34:06] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=3338072.5 Min=0 Max=3.
INFO [2021-03-11 17:34:06] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:34:13] plot_cnv_observation:Start
INFO [2021-03-11 17:34:13] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:34:13] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:34:13] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:34:13] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:34:13] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:34:14] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:34:14] Quantiles of plotted data range: 0,1,1,1.5,3
INFO [2021-03-11 17:34:14] plot_cnv_observations:Writing observation data to plot_out2//infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.observations.txt
INFO [2021-03-11 17:34:20] plot_cnv_references:Start
INFO [2021-03-11 17:34:20] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:34:21] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:34:21] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:34:21] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:34:21] Quantiles of plotted data range: 1,1,1,1,1
INFO [2021-03-11 17:34:21] plot_cnv_references:Writing reference data to plot_out2//infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.references.txt
INFO [2021-03-11 17:34:24]
STEP 21: Denoising
INFO [2021-03-11 17:34:24] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier: 1.5
INFO [2021-03-11 17:34:24] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2021-03-11 17:34:24] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds: 0.929127984793343 - 1.07318760670355
INFO [2021-03-11 17:34:28] ::plot_cnv:Start
INFO [2021-03-11 17:34:28] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=3127402.03644567 Min=0.605612335994316 Max=1.59021417195841.
INFO [2021-03-11 17:34:28] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:34:48] plot_cnv(): auto thresholding at: (0.809977 , 1.193292)
INFO [2021-03-11 17:34:48] plot_cnv_observation:Start
INFO [2021-03-11 17:34:48] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:34:48] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:34:48] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:34:48] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:34:48] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:34:49] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:34:49] Quantiles of plotted data range: 0.809977199785157,1.00115779574845,1.00115779574845,1.00115779574845,1.1932922104029
INFO [2021-03-11 17:34:50] plot_cnv_observations:Writing observation data to plot_out2//infercnv.21_denoised.observations.txt
INFO [2021-03-11 17:35:07] plot_cnv_references:Start
INFO [2021-03-11 17:35:07] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:35:08] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:35:08] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:35:08] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:35:08] Quantiles of plotted data range: 0.811707332091943,1.00115779574845,1.00115779574845,1.00115779574845,1.1932922104029
INFO [2021-03-11 17:35:08] plot_cnv_references:Writing reference data to plot_out2//infercnv.21_denoised.references.txt
INFO [2021-03-11 17:35:15]
Making the final infercnv heatmap
INFO [2021-03-11 17:35:15] ::plot_cnv:Start
INFO [2021-03-11 17:35:15] ::plot_cnv:Current data dimensions (r,c)=3898,801 Total=3127402.03644567 Min=0.605612335994316 Max=1.59021417195841.
INFO [2021-03-11 17:35:15] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 17:35:32] plot_cnv(): auto thresholding at: (0.809977 , 1.190023)
INFO [2021-03-11 17:35:32] plot_cnv_observation:Start
INFO [2021-03-11 17:35:32] Observation data size: Cells= 647 Genes= 3898
INFO [2021-03-11 17:35:33] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 17:35:33] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 17:35:33] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 17:35:33] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 17:35:33] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:35:33] Quantiles of plotted data range: 0.809977199785157,1.00115779574845,1.00115779574845,1.00115779574845,1.19002280021484
INFO [2021-03-11 17:35:34] plot_cnv_observations:Writing observation data to plot_out2//infercnv.observations.txt
INFO [2021-03-11 17:35:44] plot_cnv_references:Start
INFO [2021-03-11 17:35:44] Reference data size: Cells= 154 Genes= 3898
INFO [2021-03-11 17:35:45] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 17:35:45] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 17:35:45] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 17:35:45] Quantiles of plotted data range: 0.811707332091943,1.00115779574845,1.00115779574845,1.00115779574845,1.19002280021484
INFO [2021-03-11 17:35:45] plot_cnv_references:Writing reference data to plot_out2//infercnv.references.txt
Warning messages:
1: In dir.create(out_dir) : 'plot_out2' already exists
2: In dir.create(out_dir) : 'plot_out2' already exists
3: In dir.create(out_dir) : 'plot_out2' already exists
4: In dir.create(out_dir) : 'plot_out2' already exists
5: In dir.create(out_dir) : 'plot_out2' already exists
6: In dir.create(out_dir) : 'plot_out2' already exists
end_time <- Sys.time()
end_time
[1] "2021-03-11 17:35:48 CST"
end_time - start_time
Time difference of 1.755896 hours
pred.hesc
Error: object 'pred.hesc' not found
FeaturePlot(pbmc, features = c("COL1A2", "COL1A1", "FN1", "PSME2", "H2AFZ", "ACTB", "MALAT1", "EPCAM",
"PTPRC"))
Error in is(x, "classRepresentation") : object 'pbmc' not found