1300细胞
运行2h
> 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 [2021-03-12 17:36:32] Parsing matrix: expFile.txt
INFO [2021-03-12 17:36:38] Parsing gene order file: geneFile.txt
INFO [2021-03-12 17:36:38] Parsing cell annotations file: groupFiles.txt
INFO [2021-03-12 17:36:38] ::order_reduce:Start.
INFO [2021-03-12 17:36:38] .order_reduce(): expr and order match.
INFO [2021-03-12 17:36:38] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 13013,1329 Total=7177070 Min=0 Max=1454.
INFO [2021-03-12 17:36:38] num genes removed taking into account provided gene ordering list: 442 = 3.3966033966034% removed.
INFO [2021-03-12 17:36:38] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2021-03-12 17:36:39] 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 [2021-03-12 17:36:39] ::process_data:Start
INFO [2021-03-12 17:36:39] Creating output path plot_out2/
INFO [2021-03-12 17:36:39] Checking for saved results.
INFO [2021-03-12 17:36:39]
STEP 1: incoming data
INFO [2021-03-12 17:36:41]
STEP 02: Removing lowly expressed genes
INFO [2021-03-12 17:36:41] ::above_min_mean_expr_cutoff:Start
INFO [2021-03-12 17:36:41] Removing 9462 genes from matrix as below mean expr threshold: 0.1
INFO [2021-03-12 17:36:42] validating infercnv_obj
INFO [2021-03-12 17:36:42] There are 3109 genes and 1329 cells remaining in the expr matrix.
INFO [2021-03-12 17:36:42] no genes removed due to min cells/gene filter
INFO [2021-03-12 17:36:43]
STEP 03: normalization by sequencing depth
INFO [2021-03-12 17:36:43] normalizing counts matrix by depth
INFO [2021-03-12 17:36:43] Computed total sum normalization factor as median libsize: 1376.000000
INFO [2021-03-12 17:36:43] Adding h-spike
INFO [2021-03-12 17:36:43] -hspike modeling of ref-fib
INFO [2021-03-12 17:37:33] validating infercnv_obj
INFO [2021-03-12 17:37:33] normalizing counts matrix by depth
INFO [2021-03-12 17:37:33] Using specified normalization factor: 1376.000000
INFO [2021-03-12 17:37:34]
STEP 04: log transformation of data
INFO [2021-03-12 17:37:34] transforming log2xplus1()
INFO [2021-03-12 17:37:34] -mirroring for hspike
INFO [2021-03-12 17:37:34] transforming log2xplus1()
INFO [2021-03-12 17:37:36]
STEP 08: removing average of reference data (before smoothing)
INFO [2021-03-12 17:37:36] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-12 17:37:36] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-12 17:37:38] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-12 17:37:38] -mirroring for hspike
INFO [2021-03-12 17:37:38] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-12 17:37:38] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-12 17:37:40] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-12 17:37:43]
STEP 09: apply max centered expression threshold: 3
INFO [2021-03-12 17:37:43] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-12 17:37:43] -mirroring for hspike
INFO [2021-03-12 17:37:43] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2021-03-12 17:37:45]
STEP 10: Smoothing data per cell by chromosome
INFO [2021-03-12 17:37:45] smooth_by_chromosome: chr: chr1
INFO [2021-03-12 17:37:47] smooth_by_chromosome: chr: chr10
INFO [2021-03-12 17:37:48] smooth_by_chromosome: chr: chr11
INFO [2021-03-12 17:37:49] smooth_by_chromosome: chr: chr12
INFO [2021-03-12 17:37:50] smooth_by_chromosome: chr: chr13
INFO [2021-03-12 17:37:51] smooth_by_chromosome: chr: chr14
INFO [2021-03-12 17:37:52] smooth_by_chromosome: chr: chr15
INFO [2021-03-12 17:37:53] smooth_by_chromosome: chr: chr16
INFO [2021-03-12 17:37:55] smooth_by_chromosome: chr: chr17
INFO [2021-03-12 17:37:56] smooth_by_chromosome: chr: chr18
INFO [2021-03-12 17:37:56] smooth_by_chromosome: chr: chr19
INFO [2021-03-12 17:37:58] smooth_by_chromosome: chr: chr2
INFO [2021-03-12 17:37:59] smooth_by_chromosome: chr: chr20
INFO [2021-03-12 17:38:00] smooth_by_chromosome: chr: chr21
INFO [2021-03-12 17:38:00] smooth_by_chromosome: chr: chr22
INFO [2021-03-12 17:38:01] smooth_by_chromosome: chr: chr3
INFO [2021-03-12 17:38:02] smooth_by_chromosome: chr: chr4
INFO [2021-03-12 17:38:03] smooth_by_chromosome: chr: chr5
INFO [2021-03-12 17:38:04] smooth_by_chromosome: chr: chr6
INFO [2021-03-12 17:38:06] smooth_by_chromosome: chr: chr7
INFO [2021-03-12 17:38:07] smooth_by_chromosome: chr: chr8
INFO [2021-03-12 17:38:09] smooth_by_chromosome: chr: chr9
INFO [2021-03-12 17:38:10] -mirroring for hspike
INFO [2021-03-12 17:38:10] smooth_by_chromosome: chr: chrA
INFO [2021-03-12 17:38:10] smooth_by_chromosome: chr: chr_0
INFO [2021-03-12 17:38:10] smooth_by_chromosome: chr: chr_B
INFO [2021-03-12 17:38:11] smooth_by_chromosome: chr: chr_0pt5
INFO [2021-03-12 17:38:11] smooth_by_chromosome: chr: chr_C
INFO [2021-03-12 17:38:11] smooth_by_chromosome: chr: chr_1pt5
INFO [2021-03-12 17:38:11] smooth_by_chromosome: chr: chr_D
INFO [2021-03-12 17:38:12] smooth_by_chromosome: chr: chr_2pt0
INFO [2021-03-12 17:38:12] smooth_by_chromosome: chr: chr_E
INFO [2021-03-12 17:38:12] smooth_by_chromosome: chr: chr_3pt0
INFO [2021-03-12 17:38:12] smooth_by_chromosome: chr: chr_F
INFO [2021-03-12 17:38:16]
STEP 11: re-centering data across chromosome after smoothing
INFO [2021-03-12 17:38:16] ::center_smooth across chromosomes per cell
INFO [2021-03-12 17:38:16] -mirroring for hspike
INFO [2021-03-12 17:38:16] ::center_smooth across chromosomes per cell
INFO [2021-03-12 17:38:20]
STEP 12: removing average of reference data (after smoothing)
INFO [2021-03-12 17:38:20] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-12 17:38:20] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-12 17:38:21] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-12 17:38:22] -mirroring for hspike
INFO [2021-03-12 17:38:22] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-03-12 17:38:22] subtracting mean(normal) per gene per cell across all data
INFO [2021-03-12 17:38:23] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-03-12 17:38:27]
STEP 14: invert log2(FC) to FC
INFO [2021-03-12 17:38:27] invert_log2(), computing 2^x
INFO [2021-03-12 17:38:27] -mirroring for hspike
INFO [2021-03-12 17:38:27] invert_log2(), computing 2^x
INFO [2021-03-12 17:38:32]
STEP 15: Clustering samples (not defining tumor subclusters)
INFO [2021-03-12 17:38:32] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-12 17:38:32] define_signif_tumor_subclusters(), tumor: epi
INFO [2021-03-12 17:39:06] cut tree into: 1 groups
INFO [2021-03-12 17:39:06] -processing epi,epi_s1
INFO [2021-03-12 17:39:06] define_signif_tumor_subclusters(), tumor: ref-fib
INFO [2021-03-12 17:39:07] cut tree into: 1 groups
INFO [2021-03-12 17:39:07] -processing ref-fib,ref-fib_s1
INFO [2021-03-12 17:39:07] -mirroring for hspike
INFO [2021-03-12 17:39:07] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-03-12 17:39:07] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_ref-fib
INFO [2021-03-12 17:39:08] cut tree into: 1 groups
INFO [2021-03-12 17:39:08] -processing spike_tumor_cell_ref-fib,spike_tumor_cell_ref-fib_s1
INFO [2021-03-12 17:39:08] define_signif_tumor_subclusters(), tumor: simnorm_cell_ref-fib
INFO [2021-03-12 17:39:08] cut tree into: 1 groups
INFO [2021-03-12 17:39:08] -processing simnorm_cell_ref-fib,simnorm_cell_ref-fib_s1
INFO [2021-03-12 17:39:16] ::plot_cnv:Start
INFO [2021-03-12 17:39:16] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=4132857.85630858 Min=0.687785066303468 Max=1.36861404266677.
INFO [2021-03-12 17:39:16] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 17:39:29] plot_cnv(): auto thresholding at: (0.880033 , 1.120450)
INFO [2021-03-12 17:39:29] plot_cnv_observation:Start
INFO [2021-03-12 17:39:29] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 17:39:29] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 17:39:29] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 17:39:29] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 17:39:29] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 17:39:30] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 17:39:30] Quantiles of plotted data range: 0.880032968263692,0.971675949081899,0.99848118493735,1.02776607287257,1.12044955344194
INFO [2021-03-12 17:39:31] plot_cnv_observations:Writing observation data to plot_out2//infercnv.preliminary.observations.txt
INFO [2021-03-12 17:39:42] plot_cnv_references:Start
INFO [2021-03-12 17:39:42] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 17:39:44] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 17:39:44] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 17:39:44] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 17:39:44] Quantiles of plotted data range: 0.880032968263692,0.979733608634185,0.998467973460751,1.01930056882237,1.12044955344194
INFO [2021-03-12 17:39:44] plot_cnv_references:Writing reference data to plot_out2//infercnv.preliminary.references.txt
INFO [2021-03-12 17:39:47]
STEP 17: HMM-based CNV prediction
INFO [2021-03-12 17:39:47] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2021-03-12 17:39:48] -done predicting CNV based on initial tumor subclusters
INFO [2021-03-12 17:39:50] get_predicted_CNV_regions(subcluster)
INFO [2021-03-12 17:39:50] -processing cell_group_name: epi.epi_s1, size: 1112
INFO [2021-03-12 17:39:58] -processing cell_group_name: ref-fib.ref-fib_s1, size: 217
INFO [2021-03-12 17:40:02] -writing cell clusters file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2021-03-12 17:40:02] -writing cnv regions file: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2021-03-12 17:40:02] -writing per-gene cnv report: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2021-03-12 17:40:02] -writing gene ordering info: plot_out2//17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2021-03-12 17:40:03] ::plot_cnv:Start
INFO [2021-03-12 17:40:03] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=12999399 Min=1 Max=5.
INFO [2021-03-12 17:40:03] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 17:40:11] plot_cnv_observation:Start
INFO [2021-03-12 17:40:11] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 17:40:11] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 17:40:11] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 17:40:11] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 17:40:11] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 17:40:12] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 17:40:12] Quantiles of plotted data range: 1,3,3,4,5
INFO [2021-03-12 17:40:13] plot_cnv_observations:Writing observation data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2021-03-12 17:40:20] plot_cnv_references:Start
INFO [2021-03-12 17:40:20] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 17:40:21] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 17:40:21] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 17:40:21] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 17:40:21] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-12 17:40:21] plot_cnv_references:Writing reference data to plot_out2//infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2021-03-12 17:40:23]
STEP 18: Run Bayesian Network Model on HMM predicted CNV's
INFO [2021-03-12 17:40:23] Creating the following Directory: plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2021-03-12 17:40:23] Initializing new MCM InferCNV Object.
INFO [2021-03-12 17:40:23] validating infercnv_obj
INFO [2021-03-12 17:40:23] Total CNV's: 44
INFO [2021-03-12 17:40:23] Loading BUGS Model.
INFO [2021-03-12 17:40:23] Running Sampling Using Parallel with 4 Cores
INFO [2021-03-12 19:39:27] Obtaining probabilities post-sampling
INFO [2021-03-12 19:44:56] Gibbs sampling time: 124.543678450584 Minutes
INFO [2021-03-12 19:45:02] ::plot_cnv:Start
INFO [2021-03-12 19:45:02] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=1572918.2728191 Min=0 Max=0.94270533490389.
INFO [2021-03-12 19:45:02] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:45:02] plot_cnv_observation:Start
INFO [2021-03-12 19:45:02] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:45:02] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:45:02] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:45:02] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:45:02] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:45:03] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:45:03] Quantiles of plotted data range: 0,0,0.727825720312396,0.826088435252189,0.94270533490389
INFO [2021-03-12 19:45:04] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2021-03-12 19:45:14] plot_cnv_references:Start
INFO [2021-03-12 19:45:14] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:45:16] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:45:16] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:45:16] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:45:16] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-12 19:45:16] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2021-03-12 19:45:23] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2021-03-12 19:45:23] Removing 0 CNV(s) identified by the HMM.
INFO [2021-03-12 19:45:23] Reassigning CNVs based on state probabilities.
INFO [2021-03-12 19:45:23] Changing the following CNV's states assigned by the HMM to the following based on the CNV's state probabilities.
chr1-region_1 : 2 (P= 0.193379931673452 ) -> 1 (P= 0.502315339609754 )
chr12-region_10 : 5 (P= 0.148108865800845 ) -> 6 (P= 0.477225233268546 )
chr12-region_11 : 4 (P= 0.243490178336198 ) -> 5 (P= 0.386161526605052 )
chr13-region_14 : 5 (P= 0.258684806588398 ) -> 6 (P= 0.424835920932065 )
chr14-region_16 : 2 (P= 0.219110876298331 ) -> 1 (P= 0.444907072827185 )
chr15-region_20 : 4 (P= 0.288105781543218 ) -> 5 (P= 0.329424105834375 )
chr15-region_21 : 5 (P= 0.283508349806086 ) -> 6 (P= 0.335389553392053 )
chr2-region_42 : 1 (P= 0.147243004173674 ) -> 6 (P= 0.569070252386445 )
chr7-region_65 : 4 (P= 0.245765294302402 ) -> 5 (P= 0.301885291150393 )
chr9-region_72 : 5 (P= 0.244315857867505 ) -> 6 (P= 0.399217522472389 )
INFO [2021-03-12 19:45:23] Creating Plots for CNV and cell Probabilities.
INFO [2021-03-12 19:46:47] ::plot_cnv:Start
INFO [2021-03-12 19:46:47] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=1572918.2728191 Min=0 Max=0.94270533490389.
INFO [2021-03-12 19:46:47] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:46:47] plot_cnv_observation:Start
INFO [2021-03-12 19:46:47] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:46:47] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:46:47] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:46:47] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:46:47] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:46:48] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:46:48] Quantiles of plotted data range: 0,0,0.727825720312396,0.826088435252189,0.94270533490389
INFO [2021-03-12 19:46:49] plot_cnv_observations:Writing observation data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.observations.txt
INFO [2021-03-12 19:46:57] plot_cnv_references:Start
INFO [2021-03-12 19:46:57] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:46:58] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:46:58] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:46:58] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:46:58] Quantiles of plotted data range: 0,0,0,0,0
INFO [2021-03-12 19:46:58] plot_cnv_references:Writing reference data to plot_out2//BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.references.txt
INFO [2021-03-12 19:47:02] ::plot_cnv:Start
INFO [2021-03-12 19:47:02] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=13495351 Min=1 Max=6.
INFO [2021-03-12 19:47:02] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:47:10] plot_cnv_observation:Start
INFO [2021-03-12 19:47:10] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:47:10] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:47:10] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:47:10] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:47:10] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:47:10] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:47:10] Quantiles of plotted data range: 1,3,3,4,6
INFO [2021-03-12 19:47:11] plot_cnv_observations:Writing observation data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.observations.txt
INFO [2021-03-12 19:47:18] plot_cnv_references:Start
INFO [2021-03-12 19:47:18] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:47:19] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:47:19] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:47:19] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:47:19] Quantiles of plotted data range: 3,3,3,3,3
INFO [2021-03-12 19:47:19] plot_cnv_references:Writing reference data to plot_out2//infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.references.txt
INFO [2021-03-12 19:47:21]
STEP 19: Converting HMM-based CNV states to repr expr vals
INFO [2021-03-12 19:47:23] ::plot_cnv:Start
INFO [2021-03-12 19:47:23] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=4804065 Min=0 Max=3.
INFO [2021-03-12 19:47:23] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:47:31] plot_cnv_observation:Start
INFO [2021-03-12 19:47:31] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:47:31] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:47:32] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:47:32] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:47:32] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:47:32] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:47:32] Quantiles of plotted data range: 0,1,1,1.5,3
INFO [2021-03-12 19:47:33] plot_cnv_observations:Writing observation data to plot_out2//infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.observations.txt
INFO [2021-03-12 19:47:40] plot_cnv_references:Start
INFO [2021-03-12 19:47:40] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:47:41] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:47:41] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:47:41] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:47:41] Quantiles of plotted data range: 1,1,1,1,1
INFO [2021-03-12 19:47:41] plot_cnv_references:Writing reference data to plot_out2//infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.references.txt
INFO [2021-03-12 19:47:43]
STEP 21: Denoising
INFO [2021-03-12 19:47:43] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier: 1.5
INFO [2021-03-12 19:47:43] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2021-03-12 19:47:43] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds: 0.953996136564741 - 1.0469884911424
INFO [2021-03-12 19:47:46] ::plot_cnv:Start
INFO [2021-03-12 19:47:46] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=4138427.8695679 Min=0.687785066303468 Max=1.36861404266677.
INFO [2021-03-12 19:47:46] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:47:59] plot_cnv(): auto thresholding at: (0.881193 , 1.121986)
INFO [2021-03-12 19:47:59] plot_cnv_observation:Start
INFO [2021-03-12 19:47:59] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:47:59] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:47:59] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:47:59] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:47:59] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:48:00] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:48:00] Quantiles of plotted data range: 0.881192706117415,1.00049231385357,1.00049231385357,1.00049231385357,1.12198594368128
INFO [2021-03-12 19:48:01] plot_cnv_observations:Writing observation data to plot_out2//infercnv.21_denoised.observations.txt
INFO [2021-03-12 19:48:11] plot_cnv_references:Start
INFO [2021-03-12 19:48:11] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:48:12] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:48:12] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:48:12] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:48:12] Quantiles of plotted data range: 0.881192706117415,1.00049231385357,1.00049231385357,1.00049231385357,1.12198594368128
INFO [2021-03-12 19:48:12] plot_cnv_references:Writing reference data to plot_out2//infercnv.21_denoised.references.txt
INFO [2021-03-12 19:48:16]
Making the final infercnv heatmap
INFO [2021-03-12 19:48:17] ::plot_cnv:Start
INFO [2021-03-12 19:48:17] ::plot_cnv:Current data dimensions (r,c)=3109,1329 Total=4138427.8695679 Min=0.687785066303468 Max=1.36861404266677.
INFO [2021-03-12 19:48:17] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-03-12 19:48:29] plot_cnv(): auto thresholding at: (0.879550 , 1.120450)
INFO [2021-03-12 19:48:29] plot_cnv_observation:Start
INFO [2021-03-12 19:48:29] Observation data size: Cells= 1112 Genes= 3109
INFO [2021-03-12 19:48:29] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-03-12 19:48:29] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-03-12 19:48:29] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-03-12 19:48:30] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-03-12 19:48:30] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:48:30] Quantiles of plotted data range: 0.879550446558058,1.00049231385357,1.00049231385357,1.00049231385357,1.12044955344194
INFO [2021-03-12 19:48:31] plot_cnv_observations:Writing observation data to plot_out2//infercnv.observations.txt
INFO [2021-03-12 19:48:41] plot_cnv_references:Start
INFO [2021-03-12 19:48:41] Reference data size: Cells= 217 Genes= 3109
INFO [2021-03-12 19:48:42] plot_cnv_references:Number reference groups= 1
INFO [2021-03-12 19:48:42] plot_cnv_references:Plotting heatmap.
INFO [2021-03-12 19:48:43] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-03-12 19:48:43] Quantiles of plotted data range: 0.879550446558058,1.00049231385357,1.00049231385357,1.00049231385357,1.12044955344194
INFO [2021-03-12 19:48:43] 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] "2021-03-12 19:48:45 CST"
end_time - start_time
Time difference of 2.201758 hours