plot_mr_vs_exp

This command is used to plot DMR/MR methylation levels and gene expression for a pair of DMR and its target gene.

Optional arguments:

  • -h, –help: Show the help message and exit.

Required arguments:

  • -inGeneEXPfile IN_GENE_EXPRESSION_FILE_FROM_BPB3, –in_gene_expression_file_from_bpb3: Input file name for gene expression profiles exported by bpb3 differential_expression. The file format should be: gene_name; P-values, sample1, sample2, …

  • -inMRfolder IN_METHYLATION_FOLDER_FROM_DMR, –in_methylation_folder_from_dmr: Input file folder path for methylation data. The data should be extracted by dmr_analysis dmr_exportData based on predefined blocks or regions.

Optional arguments with default values:

  • -inGene, –in_gene_name: Target gene name for an MR/DMR region. Default value is None. Specify the target gene name for the MR/DMR region.

  • -inMR, –in_mr_id: MR/DMR ID of a target gene, such as chr1:mr1234. Default value is None. Specify the MR/DMR ID of the target gene.

  • -inFile, –in_gene_mr_file: Input file that contains both DMR/MR ID and the target gene name. It should be a tab-delimited text file, where the column labels are mr_id and gene, respectively. The file format should be the same as the export file from dTarget_methy_vs_express.py. Default value is None. Specify the input file that contains both DMR/MR ID and the target gene name.

  • -expTAB, –is_tab_delimated_file4diffExp: Specifies whether the input differential expression gene file is in the bpb3 differential_expression exported file format or a common tab-delimited file format. If set, the input gene expression file will be treated as a common tab-delimited file. Default value is False.

  • -expStartCol, –gene_expression_start_column: Start column number (e.g., 0, 1, 2, …) for samples in the gene expression profile file. Default value is 2 for bpb3 exported file. Specify the start column number for samples in the gene expression profile file.

  • -pathDepth IN_DIFFEXP_PATHDEPTH4SAMPLENAME, –in_diffExp_pathDepth4sampleName: File path depth for the column sample name. For example, if the column name is /path/folder/sample_name/.., then the depth of the sample name is the number of “/” before the sample name. Default value is 12. Specify the file path depth for the column sample name.

  • -sampleName IN_SAMPLENAME_FOR_REPLACE, –in_sampleName_for_replace IN_SAMPLENAME_FOR_REPLACE: Input file name for renaming the old sample names in the gene expression data. The first column (old_name) contains the old sample names, and the second column (new_name) contains the new names used for replacement. The default file name is sample_name4replace.tsv, which can be an empty file if no replacement is needed for sample names.

  • -dpi, –figure_resolution_dpi: Exported figure resolution in dpi. Default dpi is 60. Set the exported figure resolution in dpi.

  • -wtStr, –wildType_fileString: The first few character string that labels the file name as the Wild Type condition. For example, if the file name starts with gcb_meht1_* as the wild type control sample, then –wildType_fileString is gcb. This is the default setting in the program.

  • -output_path, –output_file_path:

Output path for exported figures. Default value is “./” (current directory). Specify the output path for exported figures.