infercnv运行测试6---21步

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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> rm(list=ls())
> options(stringsAsFactors = F)
> library(Seurat)

Seurat v4 will be going to CRAN in the near future;
 for more details, please visit https://satijalab.org/seurat/v4_changes

Warning message:
程辑包‘Seurat’是用R版本4.0.3 来建造的 
> library(ggplot2)
> library(infercnv)
Warning message:
程辑包‘infercnv’是用R版本4.0.3 来建造的 
> 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 14:20:40] Parsing matrix: expFile.txt
INFO [2021-03-11 14:20:40] Parsing gene order file: geneFile.txt
INFO [2021-03-11 14:20:41] Parsing cell annotations file: groupFiles.txt
INFO [2021-03-11 14:20:41] ::order_reduce:Start.
INFO [2021-03-11 14:20:41] .order_reduce(): expr and order match.
INFO [2021-03-11 14:20:41] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 8259,161 Total=657080 Min=0 Max=866.
INFO [2021-03-11 14:20:41] num genes removed taking into account provided gene ordering list: 302 = 3.65661702385277% removed.
INFO [2021-03-11 14:20:41] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2021-03-11 14:20:41] validating infercnv_obj
> 
> #dir.create("plot_out")#新建，原来没有这个文件夹
> 
> ##  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 14:20:41] ::process_data:Start
INFO [2021-03-11 14:20:41] Creating output path plot_out2/
INFO [2021-03-11 14:20:41] Checking for saved results.
INFO [2021-03-11 14:20:41] 

STEP 1: incoming data

INFO [2021-03-11 14:20:41]

STEP 02: Removing lowly expressed genes

INFO [2021-03-11 14:20:41] ::above_min_mean_expr_cutoff:Start
INFO [2021-03-11 14:20:41] Removing 5199 genes from matrix as below mean expr threshold: 0.1
INFO [2021-03-11 14:20:41] validating infercnv_obj
INFO [2021-03-11 14:20:41] There are 2758 genes and 161 cells remaining in the expr matrix.
INFO [2021-03-11 14:20:41] no genes removed due to min cells/gene filter
INFO [2021-03-11 14:20:42]

STEP 03: normalization by sequencing depth

INFO [2021-03-11 14:20:42] normalizing counts matrix by depth
INFO [2021-03-11 14:20:42] Computed total sum normalization factor as median libsize: 1424.000000
INFO [2021-03-11 14:20:42] Adding h-spike
INFO [2021-03-11 14:20:42] -hspike modeling of ref-fib
INFO [2021-03-11 14:21:31] validating infercnv_obj
INFO [2021-03-11 14:21:31] normalizing counts matrix by depth
INFO [2021-03-11 14:21:31] Using specified normalization factor: 1424.000000
INFO [2021-03-11 14:21:31]

STEP 04: log transformation of data

INFO [2021-03-11 14:21:31] transforming log2xplus1()
INFO [2021-03-11 14:21:31] -mirroring for hspike
INFO [2021-03-11 14:21:31] transforming log2xplus1()
INFO [2021-03-11 14:21:32]

STEP 08: removing average of reference data (before smoothing)

INFO [2021-03-11 14:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 14:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 14:21:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 14:21:33] -mirroring for hspike
INFO [2021-03-11 14:21:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 14:21:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 14:21:35] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 14:21:36]

STEP 09: apply max centered expression threshold: 3

INFO [2021-03-11 14:21:36] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 14:21:36] -mirroring for hspike
INFO [2021-03-11 14:21:36] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-11 14:21:37]

STEP 10: Smoothing data per cell by chromosome

INFO [2021-03-11 14:21:37] smooth_by_chromosome: chr: chr1
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr10
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr11
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr12
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr13
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr14
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr15
INFO [2021-03-11 14:21:38] smooth_by_chromosome: chr: chr16
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr17
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr18
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr19
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr2
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr20
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr21
INFO [2021-03-11 14:21:39] smooth_by_chromosome: chr: chr22
INFO [2021-03-11 14:21:40] smooth_by_chromosome: chr: chr3
INFO [2021-03-11 14:21:40] smooth_by_chromosome: chr: chr4
INFO [2021-03-11 14:21:40] smooth_by_chromosome: chr: chr5
INFO [2021-03-11 14:21:40] smooth_by_chromosome: chr: chr6
INFO [2021-03-11 14:21:40] smooth_by_chromosome: chr: chr7
INFO [2021-03-11 14:21:41] smooth_by_chromosome: chr: chr8
INFO [2021-03-11 14:21:41] smooth_by_chromosome: chr: chr9
INFO [2021-03-11 14:21:41] -mirroring for hspike
INFO [2021-03-11 14:21:41] smooth_by_chromosome: chr: chrA
INFO [2021-03-11 14:21:41] smooth_by_chromosome: chr: chr_0
INFO [2021-03-11 14:21:41] smooth_by_chromosome: chr: chr_B
INFO [2021-03-11 14:21:42] smooth_by_chromosome: chr: chr_0pt5
INFO [2021-03-11 14:21:42] smooth_by_chromosome: chr: chr_C
INFO [2021-03-11 14:21:42] smooth_by_chromosome: chr: chr_1pt5
INFO [2021-03-11 14:21:42] smooth_by_chromosome: chr: chr_D
INFO [2021-03-11 14:21:42] smooth_by_chromosome: chr: chr_2pt0
INFO [2021-03-11 14:21:43] smooth_by_chromosome: chr: chr_E
INFO [2021-03-11 14:21:44] smooth_by_chromosome: chr: chr_3pt0
INFO [2021-03-11 14:21:44] smooth_by_chromosome: chr: chr_F
INFO [2021-03-11 14:21:46]

STEP 11: re-centering data across chromosome after smoothing

INFO [2021-03-11 14:21:46] ::center_smooth across chromosomes per cell
INFO [2021-03-11 14:21:46] -mirroring for hspike
INFO [2021-03-11 14:21:46] ::center_smooth across chromosomes per cell
INFO [2021-03-11 14:21:47]

STEP 12: removing average of reference data (after smoothing)

INFO [2021-03-11 14:21:47] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 14:21:47] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 14:21:48] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 14:21:48] -mirroring for hspike
INFO [2021-03-11 14:21:48] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-11 14:21:48] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-11 14:21:50] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-11 14:21:51]

STEP 14: invert log2(FC) to FC

INFO [2021-03-11 14:21:51] invert_log2(), computing 2^x
INFO [2021-03-11 14:21:51] -mirroring for hspike
INFO [2021-03-11 14:21:51] invert_log2(), computing 2^x
INFO [2021-03-11 14:21:53]

STEP 15: Clustering samples (not defining tumor subclusters)

INFO [2021-03-11 14:21:53] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 14:21:53] define_signif_tumor_subclusters(), tumor: epi
INFO [2021-03-11 14:21:53] cut tree into: 1 groups
INFO [2021-03-11 14:21:53] -processing epi,epi_s1
INFO [2021-03-11 14:21:53] define_signif_tumor_subclusters(), tumor: ref-fib
INFO [2021-03-11 14:21:53] cut tree into: 1 groups
INFO [2021-03-11 14:21:53] -processing ref-fib,ref-fib_s1
INFO [2021-03-11 14:21:53] -mirroring for hspike
INFO [2021-03-11 14:21:53] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-11 14:21:53] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_ref-fib
INFO [2021-03-11 14:21:54] cut tree into: 1 groups
INFO [2021-03-11 14:21:54] -processing spike_tumor_cell_ref-fib,spike_tumor_cell_ref-fib_s1
INFO [2021-03-11 14:21:54] define_signif_tumor_subclusters(), tumor: simnorm_cell_ref-fib
INFO [2021-03-11 14:21:54] cut tree into: 1 groups
INFO [2021-03-11 14:21:54] -processing simnorm_cell_ref-fib,simnorm_cell_ref-fib_s1
INFO [2021-03-11 14:21:56] ::plot_cnv:Start
INFO [2021-03-11 14:21:56] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=444261.448584115 Min=0.7259085460275 Max=1.27974740879628.
INFO [2021-03-11 14:21:56] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:21:58] plot_cnv(): auto thresholding at: (0.882791 , 1.118216)
INFO [2021-03-11 14:21:58] plot_cnv_observation:Start
INFO [2021-03-11 14:21:58] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:21:58] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:21:58] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:21:58] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:21:58] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:21:58] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:21:58] Quantiles of plotted data range: 0.882790650772113,0.966942481185594,0.998792930197712,1.03387941341448,1.11821578824489
INFO [2021-03-11 14:21:58] plot_cnv_observations:Writing observation data to plot_out2//infercnv.preliminary.observations.txt
INFO [2021-03-11 14:21:59] plot_cnv_references:Start
INFO [2021-03-11 14:21:59] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:21:59] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:21:59] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:21:59] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:21:59] Quantiles of plotted data range: 0.882790650772113,0.978846385330733,0.998778646338114,1.02034944189329,1.11821578824489
INFO [2021-03-11 14:21:59] plot_cnv_references:Writing reference data to plot_out2//infercnv.preliminary.references.txt
INFO [2021-03-11 14:22:00]

STEP 17: HMM-based CNV prediction

INFO [2021-03-11 14:22:00] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2021-03-11 14:22:01] -done predicting CNV based on initial tumor subclusters
INFO [2021-03-11 14:22:02] get_predicted_CNV_regions(subcluster)
INFO [2021-03-11 14:22:02] -processing cell_group_name: epi.epi_s1, size: 57
INFO [2021-03-11 14:22:05] -processing cell_group_name: ref-fib.ref-fib_s1, size: 104
INFO [2021-03-11 14:22:09] -writing cell clusters file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2021-03-11 14:22:09] -writing cnv regions file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2021-03-11 14:22:09] -writing per-gene cnv report: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2021-03-11 14:22:09] -writing gene ordering info: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2021-03-11 14:22:10] ::plot_cnv:Start
INFO [2021-03-11 14:22:10] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=1375434 Min=1 Max=6.
INFO [2021-03-11 14:22:10] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:22:10] plot_cnv_observation:Start
INFO [2021-03-11 14:22:10] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:22:10] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:22:10] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:22:10] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:22:10] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:22:11] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:22:11] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-11 14:22:11] plot_cnv_observations:Writing observation data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2021-03-11 14:22:11] plot_cnv_references:Start
INFO [2021-03-11 14:22:11] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:22:11] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:22:11] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:22:11] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:22:11] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-11 14:22:11] plot_cnv_references:Writing reference data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2021-03-11 14:22:12]

STEP 18: Run Bayesian Network Model on HMM predicted CNV's

INFO [2021-03-11 14:22:12] Creating the following Directory: plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2021-03-11 14:22:12] Initializing new MCM InferCNV Object.
INFO [2021-03-11 14:22:12] validating infercnv_obj
INFO [2021-03-11 14:22:12] Total CNV's: 40
INFO [2021-03-11 14:22:12] Loading BUGS Model.
INFO [2021-03-11 14:22:12] Running Sampling Using Parallel with 4 Cores
INFO [2021-03-11 14:27:32] Obtaining probabilities post-sampling
INFO [2021-03-11 14:27:47] Gibbs sampling time: 5.58109418153763 Minutes
INFO [2021-03-11 14:27:49] ::plot_cnv:Start
INFO [2021-03-11 14:27:49] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=71012.5240103977 Min=0 Max=0.984422691407214.
INFO [2021-03-11 14:27:49] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:27:49] plot_cnv_observation:Start
INFO [2021-03-11 14:27:49] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:27:49] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:27:49] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:27:49] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:27:49] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:27:50] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:27:50] Quantiles of plotted data range: 0,0,0.654166120340874,0.837559084106656,0.984422691407214
INFO [2021-03-11 14:27:50] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2021-03-11 14:27:50] plot_cnv_references:Start
INFO [2021-03-11 14:27:50] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:27:50] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:27:50] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:27:50] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:27:50] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-11 14:27:50] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2021-03-11 14:27:53] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2021-03-11 14:27:53] Removing 0 CNV(s) identified by the HMM.
INFO [2021-03-11 14:27:53] Reassigning CNVs based on state probabilities.
INFO [2021-03-11 14:27:53] Changing the following CNV's states assigned by the HMM to the following based on the CNV's state probabilities.
chr14-region_18 : 4 (P= 0.312069975661675 ) -> 3 (P= 0.345833879659126 )
chr20-region_42 : 4 (P= 0.35482636986536 ) -> 3 (P= 0.412560026703347 )
INFO [2021-03-11 14:27:53] Creating Plots for CNV and cell Probabilities.
INFO [2021-03-11 14:28:14] ::plot_cnv:Start
INFO [2021-03-11 14:28:14] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=71012.5240103977 Min=0 Max=0.984422691407214.
INFO [2021-03-11 14:28:14] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:28:14] plot_cnv_observation:Start
INFO [2021-03-11 14:28:14] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:28:14] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:28:14] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:28:14] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:28:14] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:28:14] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:14] Quantiles of plotted data range: 0,0,0.654166120340874,0.837559084106656,0.984422691407214
INFO [2021-03-11 14:28:14] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.observations.txt
INFO [2021-03-11 14:28:15] plot_cnv_references:Start
INFO [2021-03-11 14:28:15] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:28:15] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:28:15] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:28:15] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:15] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-11 14:28:15] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.references.txt
INFO [2021-03-11 14:28:18] ::plot_cnv:Start
INFO [2021-03-11 14:28:18] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=1373439 Min=1 Max=6.
INFO [2021-03-11 14:28:18] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:28:19] plot_cnv_observation:Start
INFO [2021-03-11 14:28:19] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:28:19] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:28:19] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:28:19] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:28:19] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:28:19] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:19] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-11 14:28:19] plot_cnv_observations:Writing observation data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.observations.txt
INFO [2021-03-11 14:28:20] plot_cnv_references:Start
INFO [2021-03-11 14:28:20] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:28:20] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:28:20] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:28:20] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:20] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-11 14:28:20] plot_cnv_references:Writing reference data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.references.txt
INFO [2021-03-11 14:28:21]

STEP 19: Converting HMM-based CNV states to repr expr vals

INFO [2021-03-11 14:28:23] ::plot_cnv:Start
INFO [2021-03-11 14:28:23] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=466325 Min=0 Max=3.
INFO [2021-03-11 14:28:23] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:28:24] plot_cnv_observation:Start
INFO [2021-03-11 14:28:24] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:28:24] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:28:24] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:28:24] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:28:24] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:28:24] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:24] Quantiles of plotted data range: 0,1,1,1.5,3
INFO [2021-03-11 14:28:24] 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 14:28:24] plot_cnv_references:Start
INFO [2021-03-11 14:28:24] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:28:24] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:28:24] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:28:24] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:24] Quantiles of plotted data range: 1,1,1,1,1
INFO [2021-03-11 14:28:25] 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 14:28:25]

STEP 21: Denoising

INFO [2021-03-11 14:28:25] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier: 1.5
INFO [2021-03-11 14:28:25] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2021-03-11 14:28:25] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds: 0.950161189787372 - 1.05101839800469
INFO [2021-03-11 14:28:27] ::plot_cnv:Start
INFO [2021-03-11 14:28:27] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=444846.118740976 Min=0.7259085460275 Max=1.27974740879628.
INFO [2021-03-11 14:28:27] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:28:28] plot_cnv(): auto thresholding at: (0.885424 , 1.118216)
INFO [2021-03-11 14:28:29] plot_cnv_observation:Start
INFO [2021-03-11 14:28:29] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:28:29] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:28:29] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:28:29] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:28:29] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:28:29] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:29] Quantiles of plotted data range: 0.885424074744207,1.00058979389603,1.00058979389603,1.00058979389603,1.11821578824489
INFO [2021-03-11 14:28:29] plot_cnv_observations:Writing observation data to plot_out2//infercnv.21_denoised.observations.txt
INFO [2021-03-11 14:28:29] plot_cnv_references:Start
INFO [2021-03-11 14:28:29] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:28:30] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:28:30] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:28:30] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:30] Quantiles of plotted data range: 0.885424074744207,1.00058979389603,1.00058979389603,1.00058979389603,1.11821578824489
INFO [2021-03-11 14:28:30] plot_cnv_references:Writing reference data to plot_out2//infercnv.21_denoised.references.txt
INFO [2021-03-11 14:28:32]

Making the final infercnv heatmap

INFO [2021-03-11 14:28:32] ::plot_cnv:Start
INFO [2021-03-11 14:28:32] ::plot_cnv:Current data dimensions (r,c)=2758,161 Total=444846.118740976 Min=0.7259085460275 Max=1.27974740879628.
INFO [2021-03-11 14:28:32] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-11 14:28:34] plot_cnv(): auto thresholding at: (0.881784 , 1.118216)
INFO [2021-03-11 14:28:34] plot_cnv_observation:Start
INFO [2021-03-11 14:28:34] Observation data size: Cells= 57 Genes= 2758
INFO [2021-03-11 14:28:34] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-11 14:28:34] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-11 14:28:34] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-11 14:28:34] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-11 14:28:34] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:34] Quantiles of plotted data range: 0.881784211755114,1.00058979389603,1.00058979389603,1.00058979389603,1.11821578824489
INFO [2021-03-11 14:28:34] plot_cnv_observations:Writing observation data to plot_out2//infercnv.observations.txt
INFO [2021-03-11 14:28:35] plot_cnv_references:Start
INFO [2021-03-11 14:28:35] Reference data size: Cells= 104 Genes= 2758
INFO [2021-03-11 14:28:35] plot_cnv_references:Number reference groups= 1
INFO [2021-03-11 14:28:35] plot_cnv_references:Plotting heatmap.
INFO [2021-03-11 14:28:35] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-11 14:28:35] Quantiles of plotted data range: 0.881784211755114,1.00058979389603,1.00058979389603,1.00058979389603,1.11821578824489
INFO [2021-03-11 14:28:35] 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
7: In dir.create(out_dir) : 'plot_out2' already exists

end_time <- Sys.time()
end_time - start_time
Time difference of 7.921937 mins
end_time
[1] "2021-03-11 14:28:36 CST"
end_time - start_time
Time difference of 7.921937 mins

耗时步骤18 约5分钟

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