cnv_visual.RdThis function is designed to custom plot CNVs, it now support to visualize CNVs by Chromosome, Interested Individual, Interested Region, Target Gene, et al.
cnv_visual( clean_cnv, max_chr = NULL, chr_id = NULL, species = NULL, start_position = NULL, end_position = NULL, individual_id = NULL, target_gene = NULL, max_chr_length = 160, refgene = NULL, plot_title = NULL, report_id = NULL, pedigree = NULL, show_name = c(0, 160), width_1 = 13, height_1 = 10, folder = "cnv_visual", col_0 = "hotpink", col_1 = "turquoise", col_2 = "gray", col_3 = "tomato", col_4 = "deepskyblue", col_gene = "gray", gene_font_size = 2.2 )
| clean_cnv | cnv list file, standard file was generated by 'cnv_clean' function |
|---|---|
| max_chr | the maximum number of chromosomes to plot, it used for plot all chromosomes at once |
| chr_id | the number of chromosome want to plot |
| species | which species in the input data, unused at the moment |
| start_position | decimal digit, default unit is 'Mb'. such as 23.2112 |
| end_position | decimal digit, default unit is 'Mb'. such as 23.2112 |
| individual_id | the ID of individual in cnv list, used to plot all chromosome for specific Individual |
| target_gene | the |
| max_chr_length | the maximum length of chromosome, default unit is 'Mb' |
| refgene | if true, will plot gene above the CNV plot, need to combine with the clean_cnv, and the stardard clean_cnv file need the annotated cnv list which was generated from call_gene function, internal reference gene-list are "ARS_ens", "ARS_UCSC" and "UMD_UCSC". Or provide the reference genes list corresponding to your data |
| plot_title | set the title of final plot |
| report_id | report the sample ID while plotting |
| pedigree | pedigree list, require at least three columns, Sample_Id, Sire and Dam |
| show_name | default value is show_name = c(0, 160). accept the vectors only, unit is Mb. for example show_name = c(11.2, 12.4, 15.3, 18.4), means only plot the genes within the given interval |
| width_1 | number to set the width of final plot size, unit is 'cm' |
| height_1 | number to set the height of final plot size, unit is 'cm' |
| folder | set the name of folder to save results |
| col_0 | set color for 0 copy of CNV |
| col_1 | set color for 1 copy of CNV |
| col_2 | set color for 2 copy of CNV (which might be ROH) |
| col_3 | set color for 3 copy of CNV |
| col_4 | set color for 4 copy of CNV |
| col_gene | set the color of Gene, only work in Gene annotated at CNV plot |
| gene_font_size | set the size of Gene in CNV Annotation plot |
CNV distribution plot