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library(circlize)
library(ComplexHeatmap)
library(GetoptLong)
mat = read.table(textConnection(
"s1,s2,s3
g1,snv;indel,snv,indel
g2,,snv;indel,snv
g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)
mat = as.matrix(mat)
get_type_fun = function(x) strsplit(x, ";")[[1]]
alter_fun = list(
snv = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.9,
gp = gpar(fill = col["snv"], col = NA)),
indel = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.4,
gp = gpar(fill = col["indel"], col = NA))
)
col = c(snv = "red", indel = "blue")
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col)
draw(ht)
## turn off row names while turn on column names
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
show_column_names = TRUE, show_row_names = FALSE, show_pct = FALSE)
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col, pct_side = "right",
row_names_side = "left")
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
top_annotation = HeatmapAnnotation(column_barplot = anno_oncoprint_barplot())
)
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
top_annotation = HeatmapAnnotation(
column_barplot = anno_oncoprint_barplot(),
foo = 1:3,
annotation_name_side = "left")
)
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
top_annotation = HeatmapAnnotation(
cbar = anno_oncoprint_barplot(),
foo1 = 1:3,
annotation_name_side = "left"),
left_annotation = rowAnnotation(foo2 = 1:3),
right_annotation = rowAnnotation(cbar = anno_oncoprint_barplot(), foo3 = 1:3),
)
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
top_annotation = HeatmapAnnotation(
cbar = anno_oncoprint_barplot(border = TRUE),
foo1 = 1:3,
annotation_name_side = "left"),
left_annotation = rowAnnotation(foo2 = 1:3),
right_annotation = rowAnnotation(
cbar = anno_oncoprint_barplot(border = TRUE),
foo3 = 1:3),
)
draw(ht)
ht = oncoPrint(mat, get_type = get_type_fun,
alter_fun = alter_fun, col = col,
right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot(axis_param = list(side = "bottom", labels_rot = 90)))
)
draw(ht)
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