chisel-plotting.md

Command chisel-plotting.py

The CHISEL command chisel-plotting.py generates several useful plots, which can be used to inspect the inferred results or for quality control. More specifically, this command generates 15 plots.

Main plots

Allele-specific copy numbers

This plot (allelecn.png) depicts the allele-specific copy numbers inferred by CHISEL for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap represent the difference pairs of allele-specific copy numbers and a full description of the color map used is available in the CHISEL manuscript.

Corrected allele-specific copy numbers

This plot (allelecn-corrected.png) depicts the allele-specific copy numbers inferred by CHISEL and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap represent the difference pairs of allele-specific copy numbers and a full description of the color map used is available in the CHISEL manuscript.

Haplotype-specific copy numbers

This plot (haplotypecn.png) depicts the haplotype-specific copy numbers inferred by CHISEL for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap represent the haplotype of the allele with fewer copies, such that green and magenta represent haplotype A and B, respectively. Note that balanced regions (allele with the same number of copies) are represented in white. Further descriptions of the color map used are available in the CHISEL manuscript.

Corrected haplotype-specific copy numbers

This plot (haplotypecn-corrected.png) depicts the haplotype-specific copy numbers inferred by CHISEL and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap represent the haplotype of the allele with fewer copies, such that green and magenta represent haplotype A and B, respectively. Note that balanced regions (allele with the same number of copies) are represented in white. Further descriptions of the color map used are available in the CHISEL manuscript.

Useful additional plots

BAF and RDR plots

This plot (rbplot_mirrored.png) shows the global clusters of RDRs and BAFs inferred for a random sample of a certain number of cells (by default 20 cells). Each plot corresponds to a different cell, with each plot depicting the bins (each point) which are represented by the corresponding values of |0.5 - mirrored BAF| (x-axis) and RDR (y-axis), and are colored according to the corresponding cluster; note that colors are consistent across cells.

Clustered RDR

This plot (crdr.png) shows the estimated RDR and their cluster for a random sample of a certain number of cells (by default 20 cells). Each plot corresponds to a different cell, with each plot depicting the bins (each point) which are represented by the corresponding values of RDR (y-axis) along the entire genome (x-axis) and are colored according to the corresponding cluster; note that colors are consistent across cells.

Clustered mirrored BAF

This plot (cbaf.png) shows the estimated BAF and their cluster for a random sample of a certain number of cells (by default 20 cells). Each plot corresponds to a different cell, with each plot depicting the bins (each point) which are represented by the corresponding values of |0.5 - mirrored BAF| (y-axis) along the entire genome (x-axis) and are colored according to the corresponding cluster; note that colors are consistent across cells.

Total copy numbers

This plot (totalcn.png) is an heatmap that shows the total copy numbers inferred by CHISEL for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. Each point of the heatmap this represents the total copy numbers inferred by CHISEL, such that grey represents 2 copies, blue colors represent <2 copies with darker colors corresponding to smaller values, and red colors represent >2 copies with darker colors corresponding to higher values.

Corrected total copy numbers

This plot (totalcn-corrected.png) is an heatmap that shows the total copy numbers inferred by CHISEL and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. Each point of the heatmap this represents the total copy numbers inferred by CHISEL, such that grey represents 2 copies, blue colors represent <2 copies with darker colors corresponding to smaller values, and red colors represent >2 copies with darker colors corresponding to higher values.

LOH

This plot (loh.png) is an heatmap that shows the LOH inferred by CHISEL for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. Each point of the heatmap is colored according to the absence (white) or presence (black) of a LOH in the corresponding cell and bin.

Corrected LOH

This plot (loh-corrected.png) is an heatmap that shows the LOH inferred by CHISEL and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. Each point of the heatmap is colored according to the absence (white) or presence (black) of a LOH in the corresponding cell and bin.

A-specific copy numbers

This plot (Aspecificcn.png) is an heatmap that shows the copy numbers inferred by CHISEL for haplotype A for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap are the same for the total copy-numbers (see above).

Corrected A-specific copy numbers

This plot (Aspecificcn-corrected.png) is an heatmap that shows the copy numbers inferred by CHISEL for haplotype A and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap are the same for the total copy-numbers (see above).

B-specific copy numbers

This plot (Bspecificcn.png) is an heatmap that shows the copy numbers inferred by CHISEL for haplotype B for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap are the same for the total copy-numbers (see above).

Corrected B-specific copy numbers

This plot (Bspecificcn-corrected.png) is an heatmap that shows the copy numbers inferred by CHISEL for haplotype B and corrected using the inferred clones for every cell (rows) along the entire genome (y-axis), with cells/rows colored according to the inferred clone and columns/genomic bins colored according to the chromosome. The colors of the heatmap are the same for the total copy-numbers (see above).