GeorgescuC
commented
1 year ago Hi @sukyorsuki ,
Those files are generated at the same type as the plots if the "write_expr_matrix" option is set to TRUE, but the default is now set to FALSE and properly linked with plot_cnv. If you simply restart the same run of infercnv you already did but changing this option, it should reload a backup from the end of the process and simply plot the figure again while this time outputting the files.
If you would like that to be done for other steps as well, you can manually call plot_cnv() with that option using the backup from the given step. For the other options used in plotting (mostly for the HMM steps), you can check the call used in run() in R/infercnv_ops.R
Regards, Christophe.
I ran my scRNA-seq successfully, but failed to find the infercnv.observations.txt; infercnv.references.txt. The lattest file were listed as follows:
My R script:
infercnv_obj = infercnv::run(inferobj, cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir=outdir_1, cluster_by_groups=TRUE, denoise=TRUE, plot_steps =T, HMM=TRUE, hclust_method="ward.D2"
...
Making the final infercnv heatmap
INFO [2022-11-29 17:30:55] ::plot_cnv:Start INFO [2022-11-29 17:30:55] ::plot_cnv:Current data dimensions (r,c)=4296,4487 Total=19287731.1696059 Min=0.61200616140138 Max=1.60128649787314. INFO [2022-11-29 17:30:55] ::plot_cnv:Depending on the size of the matrix this may take a moment. INFO [2022-11-29 17:30:55] plot_cnv(): auto thresholding at: (0.851220 , 1.148780) INFO [2022-11-29 17:30:56] plot_cnv_observation:Start INFO [2022-11-29 17:30:56] Observation data size: Cells= 4339 Genes= 4296 INFO [2022-11-29 17:30:56] plot_cnv_observation:Writing observation groupings/color. INFO [2022-11-29 17:30:56] plot_cnv_observation:Done writing observation groupings/color. INFO [2022-11-29 17:30:56] plot_cnv_observation:Writing observation heatmap thresholds. INFO [2022-11-29 17:30:56] plot_cnv_observation:Done writing observation heatmap thresholds. INFO [2022-11-29 17:30:58] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000 INFO [2022-11-29 17:30:58] Quantiles of plotted data range: 0.851220076500678,1.00069872790796,1.00069872790796,1.00069872790796,1.14877992349932 INFO [2022-11-29 17:31:01] plot_cnv_references:Start INFO [2022-11-29 17:31:01] Reference data size: Cells= 148 Genes= 4296 INFO [2022-11-29 17:31:01] plot_cnv_references:Number reference groups= 1 INFO [2022-11-29 17:31:01] plot_cnv_references:Plotting heatmap. INFO [2022-11-29 17:31:01] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000 INFO [2022-11-29 17:31:01] Quantiles of plotted data range: 0.851220076500678,1.00069872790796,1.00069872790796,1.00069872790796,1.14877992349932 Warning messages: 1: Requested number is larger than the number of available items (56). Setting to 56. 2: Requested number is larger than the number of available items (56). Setting to 56. 3: Requested number is larger than the number of available items (56). Setting to 56. 4: Requested number is larger than the number of available items (56). Setting to 56. 5: Requested number is larger than the number of available items (56). Setting to 56. 6: Requested number is larger than the number of available items (55). Setting to 55. 7: Requested number is larger than the number of available items (55). Setting to 55. 8: Requested number is larger than the number of available items (55). Setting to 55. 9: Requested number is larger than the number of available items (55). Setting to 55. 10: Requested number is larger than the number of available items (55). Setting to 55.