Hi I am trying to make waterfall plot using GenVisR as shown here. I just put an example data like
sample gene_name amino.acid.change trv_type TCGA-BH-A0WA-01 BRCA1 X1559_splice splice_site_del TCGA-AN-A0XU-01 BRCA1 G1788V missense TCGA-A2-A25B-01 BRCA1 E720* nonsense TCGA-D8-A27M-01 BRCA1 P1614Qfs*19 frame_shift_del TCGA-E9-A1NC-01 BRCA1 Q139* nonsense TCGA-C8-A12T-01 BRCA1 D1344H missense TCGA-A2-A4S0-01 BRCA1 K50T missense TCGA-LL-A5YP-01 BRCA1 D96H missense TCGA-PE-A5DE-01 BRCA1 E1419K missense TCGA-A1-A0SI-01 BRCA1 E9Q missense TCGA-AO-A1KR-01 BRCA1 C644del in_frame_del TCGA-E2-A1L9-01 BRCA1 S1027I missense TCGA-EW-A2FR-01 BRCA1 D366N missense
and getting plot as shown here:
But in that, I did not understand how it is plotting translational effect, because there is no information regarding synonymous or non-synonyms mutations.