plotCSprofile ============= This tool calculates scores per genome regions and creates a profile plot for scores over sets of genomic regions. Typically, the genome regions are genes, but any other regions defined in a BED file can be used. A chromatin state segmentation generated by chromIDEAS or ideasCS is required. To learn more about the specific parameters, type: .. code-block:: sh $ plotCSprofile TSS -h OR $ plotCSprofile Body -h .. note:: - plotCSprofile TSS: In TSS mode, only those genomicpositions before (upstream) and/or after (downstream) of the TSS will be plotted. - plotCSprofile Body: In Body mode, all regions are stretched or shrunken to the length indicated by the user. Content ======= .. contents:: :local: plotCSprofile TSS Mode ^^^^^^^^^^^^^^^^^^^^^^ Required arguments """""""""""""""""" ``-i `` chromatin state segmentation file (space delimited) generated by chromIDEAS or ideasCS **[Default: None]**. Example:: #ID CHR POSst POSed cell1 cell2 1 chr1 792600 792800 1 1 2 chr1 792800 793000 0 0 3 chr1 793000 793200 0 0 4 chr1 793200 793400 0 0 ``-o `` File name to save the image. The file ending will be used to determine the image format. The available options are: "png", "jpg", "pdf" and "svg", e.g., MyHeatmap.png. **[Default: None]** ``-r `` File name or names, in BED or GTF format, containing the regions to plot. The GTF format is recommended. To ensure result accuracy, for BED format inputs, it is required to include strand information in column 4. If the strand is uncertain, use '*' to represent it **[Default: None]**. Example:: chr1 100 500 + chr3 600 900 * ... Optional arguments """""""""""""""""" ``-S `` Specify the sample ID(s) to plot the distribution curve. The ID(s) must match those in ````. If multiple sample IDs need to be specified simultaneously, separate them with commas, e.g., "sample1,sample2,sample3". **[Default: All]** ``-m `` File name to save the underlying data for the chromatin state profile. Users can use this matrix to replot the data with other software (e.g., R). **[Default: None]** ``-t `` When ```` is specified as a GTF file, select whether to use gene or transcript coordinates for analysis. **[Default: transcript]** ``-u `` Number of bins covering the upstream region of the transcription start site. **[Default: 5]** ``-d `` Number of bins covering the downstream region of the transcription end site. **[Default: 5]** ``-l `` only for TSS mode] Label shown in the plot for the TSS. Default is the **TSS**, but could be anything, e.g. "peak start". ``-z `` Mode for calculating chromatin state proportions. Possible choices: "genomic" and "state". "genomic" will compute the local proportion of each chromatin state at every site. (Example: For Site 1 with 100 "S1" out of 1,000 total values → "S1" = 100/1,000 = 10%); "state" will compute the global contribution of each site to a state’s total occurrences. (Example: If "S1" occurs 50,000 times genome-wide, Site 1’s 100 "S1" values contribute :100/50,000 = 0.2%). **[Default: genomic]** ``-W `` Plot width in Inch. **[Default: 10]** ``-H `` Plot height in Inch. **[Default: 8]** ``-C `` List of colors to use for the plotted lines. Color names and html hex strings (e.g., #eeff22) are accepted. The color names should be commas separated, e.g., red,blue. **[Default: Auto]** ``-N `` Number of plots per row. **[Default: 5]** ``-O `` Plot ordering scheme. Available options: (1) By chromatin state name (cs); (2) By chromatin state genomic percentage (csgp); (3) Custom order (comma-separated, e.g., s3,s1,s2). **[Default: cs]** ``-R`` Reverse the plot ordering scheme. ``-p `` Number of parallel processes. **[Default: 4]** ``-h`` Show this help message and exit. ``-v`` Show program's version number and exit. plotCSprofile Body Mode ^^^^^^^^^^^^^^^^^^^^^^^ Required arguments """""""""""""""""" ``-i `` chromatin state segmentation file (space delimited) generated by chromIDEAS or ideasCS **[Default: None]**. Example:: #ID CHR POSst POSed cell1 cell2 1 chr1 792600 792800 1 1 2 chr1 792800 793000 0 0 3 chr1 793000 793200 0 0 4 chr1 793200 793400 0 0 ``-o `` File name to save the image. The file ending will be used to determine the image format. The available options are: "png", "jpg", "pdf" and "svg", e.g., MyHeatmap.png. **[Default: None]** ``-r `` File name or names, in BED or GTF format, containing the regions to plot. The GTF format is recommended. To ensure result accuracy, for BED format inputs, it is required to include strand information in column 4. If the strand is uncertain, use '*' to represent it **[Default: None]**. Example:: chr1 100 500 + chr3 600 900 * ... Optional arguments """""""""""""""""" ``-S `` Specify the sample ID(s) to plot the distribution curve. The ID(s) must match those in ````. If multiple sample IDs need to be specified simultaneously, separate them with commas, e.g., "sample1,sample2,sample3". **[Default: All]** ``-m `` File name to save the underlying data for the chromatin state profile. Users can use this matrix to replot the data with other software (e.g., R). **[Default: None]** ``-t `` When ```` is specified as a GTF file, select whether to use gene or transcript coordinates for analysis. **[Default: transcript]** ``-b `` only for Body mode] Specify the number of bins for dividing the gene body region. **[Default: 10]** ``-u `` Number of bins covering the upstream region of the transcription start site. **[Default: 5]** ``-d `` Number of bins covering the downstream region of the transcription end site. **[Default: 5]** ``-s `` only for Body mode] Label shown in the plot for the start of the region. **[Default: TSS]** ``-e `` only for Body mode] Label shown in the plot for the region end. **[Default: TES]** ``-z `` Mode for calculating chromatin state proportions. Possible choices: "genomic" and "state". "genomic" will compute the local proportion of each chromatin state at every site. (Example: For Site 1 with 100 "S1" out of 1,000 total values → "S1" = 100/1,000 = 10%); "state" will compute the global contribution of each site to a state’s total occurrences. (Example: If "S1" occurs 50,000 times genome-wide, Site 1’s 100 "S1" values contribute :100/50,000 = 0.2%). **[Default: genomic]** ``-W `` Plot width in Inch. **[Default: 10]** ``-H `` Plot height in Inch. **[Default: 8]** ``-C `` List of colors to use for the plotted lines. Color names and html hex strings (e.g., #eeff22) are accepted. The color names should be commas separated, e.g., red,blue. **[Default: Auto]** ``-N `` Number of plots per row. **[Default: 5]** ``-O `` Plot ordering scheme. Available options: (1) By chromatin state name (cs); (2) By chromatin state genomic percentage (csgp); (3) Custom order (comma-separated, e.g., s3,s1,s2). **[Default: cs]** ``-R`` Reverse the plot ordering scheme. ``-p `` Number of parallel processes. **[Default: 4]** ``-h`` Show this help message and exit. ``-v`` Show program's version number and exit.