This is to create oncoprints of variants (mutations [required], copy number variants [optional], structural variants [optional]). Look at the example file and documentation for an example of how to call the function.

Simple example:

source("./generate_complex_oncoprint.R")

ht <-  generate_complex_oncoprint(muts= MUT, 

                                show.sample.names = TRUE, show.border= FALSE,

                                min.freq= 1, show.title= TRUE, title.str=  "Example 1 - YOHOOOO oncoprint with NO ERROR!", 

                                save.name= "Example_1.A",

                                save.path= "./example_oncoprints/") 

Feb 2019: features added to show RESPONSE, and SAMPLE.SOURCE (for example you can choose B-cell, T-cell, or you can even pass on the disease type such as PV, ET, etc.). Also, for timepoint data, you have the option to show a heatbar of samples that belong to the same patient. Sep 2019: new features added to allow defining the second annotation ribbon as wish (e.g., RACE or DISEASE). Other visualization added and will be explained in an analysis session. You can install/upgrade using:

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ComplexHeatmap")

Current recognized terms for mutation/CNV/SV types (col EFFECT) are:

[1] "amp" "amplification" "CN-del" "CN-gain" "complex"
[6] "complex_change_in_transcript" "complex_karyotype" "del" "deletion" "frame_shift_del"
[11] "frame_shift_ins" "frameshift_del" "frameshift_indel" "frameshift_insertion" "frameshift_variant"
[16] "fus" "fusion" "gain" "in_frame_del" "in_frame_ins"
[21] "inconclusive" "inframe_codon_gain" "inframe_codon_loss" "inframe_deletion" "inframe_indel"
[26] "inframe_insersion" "inframe_variant" "initiator_codon_change" "inv" "inversion"
[31] "karyotypic_abnormal" "LOH" "loss" "missense" "missense_codon"
[36] "missense_mutation" "N_E" "N/A" "N/E" "non_synonymous_codon"
[41] "nonsense_mutation" "nonstop_mutation" "normal" "normal_karyotype" "other_cnvs"
[46] "other_snvs" "other_svs" "rearr" "rearrangement" "rearrangements"
[51] "splice_site" "splice_site_variant" "stop_gain" "stop_gained" "stop_lost"
[56] "stop_retained_variant" "tandem dup" "tandem duplications" "tandem_duplications" "trans"
[61] "translation_start_site" "translocation" "unavailable" "unknown"

IMPORTANT:

Please contact rahnaman@mskcc.org if you had any mutation-type that wanted to have a specific representation for it in Oncoprint.