lollipopPlot2 {maftools} | R Documentation |
Compare two lollipop plots
lollipopPlot2(m1, m2, gene = NULL, AACol1 = NULL, AACol2 = NULL, m1_name = NULL, m2_name = NULL, m1_label = NULL, m2_label = NULL, refSeqID = NULL, proteinID = NULL, labPosAngle = 0, labPosSize = 0.9, colors = NULL, axisTextSize = c(1, 1), pointSize = 1.2, domainLabelSize = 1, legendTxtSize = 1)
m1 |
first |
m2 |
second |
gene |
HGNC symbol for which protein structure to be drawn. |
AACol1 |
manually specify column name for amino acid changes in m1. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'. |
AACol2 |
manually specify column name for amino acid changes in m2. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'. |
m1_name |
name for |
m2_name |
name for |
m1_label |
Amino acid positions to label for |
m2_label |
Amino acid positions to label for |
refSeqID |
RefSeq transcript identifier for |
proteinID |
RefSeq protein identifier for |
labPosAngle |
angle for labels. Defaults to horizonal 0 degree labels. Set to 90 for vertical; 45 for diagonal labels. |
labPosSize |
Text size for labels. Default 3 |
colors |
named vector of colors for each Variant_Classification. Default NULL. |
axisTextSize |
text size for axis labels. Default 1. |
pointSize |
size of lollipop heads. Default 1.2 |
domainLabelSize |
text size for domain labels. Default 1. |
legendTxtSize |
Default 1. |
Draws lollipop plot for a gene from two cohorts
primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools") relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools") primary.apl <- read.maf(maf = primary.apl) relapse.apl <- read.maf(maf = relapse.apl) lollipopPlot2(m1 = primary.apl, m2 = relapse.apl, gene = "FLT3",AACol1 = "amino_acid_change", AACol2 = "amino_acid_change", m1_name = "Primary", m2_name = "Relapse")