Plotting inferCNV heatmap of several samples

[farhadfaghihi4]

Hi everyone,

I am analyzing my scRNA-seq data and I have 12 samples. I have run inferCNV on each one of my samples and have all the results.
Now I want to combine all the results and draw a heatmap that illustrates the CNV score of each cell in each genomic region, exactly like the picture below.
However, the problem is that I cannot find the data that shows the CNV score of each cell in each genomic region.
I would greatly appreciate your help if you could solve this issue for me.

Best

[nbahti]

Could you solve this problem? I have a similar task to do.

[farhadfaghihi4]

Unfortunately, I could not solve this yet.

[SukuraAddiction]

I have a similar question as well. Have you solved it?

[farhadfaghihi4]

Unfortunately, not yet.

[ZHawul]

My solution for this has been to run all the samples as a single dataset but then append the patient IDs to the cells of interest in the annotation dataframe. Here is the code I used to add the patient IDs with an example of what the output looks like. I'm sure you could probably also do this when making the annotaiotn dataframe and add the patient_ID to all cell types but i just wanted to add it to the query cells.

annotation_df <- data.frame(barcodes = rownames([email protected]),
                            annotation = [email protected][cell_type_col_name])
for (i in 1:length(annotation_df$Cell_Type)) {
  if(annotation_df$Cell_Type[i] == "Tumour Cell"){
    annotation_df$Cell_Type[i] = paste(annotation_df$Cell_Type[i], 
                                             subset_data$Patient_ID[i], 
                                             sep="_")}
}

[farhadfaghihi4]

Thanks @ZHawul.
But the issue is still there. The plot that you have attached is different from the one that I want to generate.