oncoPrint() (ComplexHeatmap) will just plot whatever data you provide, whether it be related to cockroach counts, vaccine rates per nation, or mutations per single gene or multiple genes. You just have to structure the data as you wish for it to be plotted.

This should help you to get started:

df
                Gene Alteration Type
TCGA-2Y-A9GW-01 FLT3         UP  EXP
TCGA-2Y-A9GY-01 FLT3         UP  EXP
TCGA-2Y-A9H2-01 FLT3         UP  EXP
...
TCGA-BC-A10W-01 FLT3       DOWN  EXP
TCGA-BC-A110-01                     
...
TCGA-BD-A3ER-01                     
TCGA-BW-A5NQ-01                     


require(ComplexHeatmap)
require(circlize)

define the colours and box-sizes for each category in the oncoprint

alter_fun <- list(
    EXP=function(x, y, w, h)
    {
        grid.rect(x, y, w*0.9, h*0.9, gp=gpar(fill="black", col=NA))
    },
    UP=function(x, y, w, h)
    {
        grid.rect(x, y, w*0.5, h*0.5, gp=gpar(fill="forestgreen", col=NA))
    },
    DOWN=function(x, y, w, h)
    {
        grid.rect(x, y, w*0.5, h*0.5, gp=gpar(fill="purple", col=NA))
    }
)

cols <- c("EXP"="black", "UP"="forestgreen", "DOWN"="purple")

plot annotations separately

onco <- oncoPrint(df[,2:3],
    name="MyOncoprint",
    alter_fun=alter_fun,
    col=cols,
    remove_empty_columns=FALSE,

    row_title="Row title",
    row_title_side="left",
    row_title_gp=gpar(fontsize=15, fontface="bold"),
    show_row_names=TRUE,
    row_names_gp=gpar(fontsize=16, fontface="bold"),
    row_names_max_width=unit(6, "cm"),

    column_title="Column title",
    column_title_side="top",
    column_title_gp=gpar(fontsize=15, fontface="bold"),
    column_title_rot=0,
    show_column_names=TRUE,
    column_names_gp=gpar(fontsize=15, fontface="bold"),

    pct_gp=gpar(fontsize=15, fontface="bold", fill="white", col="white"),
    axis_gp=gpar(fontsize=15, fontface="bold"),

    heatmap_legend_param=list(
        title="My legend",
        title_gp=gpar(fontsize=15, fontface="bold"),
        at=c("EXP", "UP", "DOWN"),
        labels=c("EXP", "UP", "DOWN"),
        labels_gp=gpar(fontsize=15, fontface="bold"),
        nrow=1,
        title_position="topcenter"))

draw(onco, heatmap_legend_side="top", annotation_legend_side="bottom", newpage=FALSE)

merge the annotations and split by semi-colon

Here, we add a single extra parameter to oncoPrint(): get_type

df.new <- df
df.new$AlterationType <- apply(df.new, 1, function(x) paste(x[2], x[3], sep=";"))
df.new <- data.frame(df.new[,4], row.names=rownames(df))
colnames(df.new) <- "AlterationType"
df.new

                AlterationType
TCGA-2Y-A9GW-01         UP;EXP
TCGA-2Y-A9GY-01         UP;EXP
TCGA-2Y-A9H2-01         UP;EXP
TCGA-2Y-A9H7-01       DOWN;EXP
TCGA-5C-A9VG-01       DOWN;EXP
TCGA-5C-A9VH-01       DOWN;EXP
TCGA-5R-AA1C-01       DOWN;EXP
TCGA-5R-AA1D-01         UP;EXP
TCGA-BC-4072-01         UP;EXP
TCGA-BC-A10Q-01       DOWN;EXP
TCGA-BC-A10W-01       DOWN;EXP
TCGA-BC-A110-01              ;
TCGA-BC-A5W4-01              ;
TCGA-BC-A69H-01              ;
TCGA-BD-A3ER-01              ;
TCGA-BW-A5NQ-01              ;


onco <- oncoPrint(df.new,
    get_type=function(x) strsplit(x, ";")[[1]],

    name="MyOncoprint",
    alter_fun=alter_fun,
    col=cols,
    remove_empty_columns=FALSE,

    row_title="Row title",
    row_title_side="left",
    row_title_gp=gpar(fontsize=15, fontface="bold"),
    show_row_names=TRUE,
    row_names_gp=gpar(fontsize=16, fontface="bold"),
    row_names_max_width=unit(6, "cm"),

    column_title="Column title",
    column_title_side="top",
    column_title_gp=gpar(fontsize=15, fontface="bold"),
    column_title_rot=0,
    show_column_names=TRUE,
    column_names_gp=gpar(fontsize=15, fontface="bold"),

    pct_gp=gpar(fontsize=15, fontface="bold", fill="white", col="white"),
    axis_gp=gpar(fontsize=15, fontface="bold"),

    heatmap_legend_param=list(
        title="My legend",
        title_gp=gpar(fontsize=15, fontface="bold"),
        at=c("EXP", "UP", "DOWN"),
        labels=c("EXP", "UP", "DOWN"),
        labels_gp=gpar(fontsize=15, fontface="bold"),
        nrow=1,
        title_position="topcenter"))

draw(onco, heatmap_legend_side="top", annotation_legend_side="bottom", newpage=FALSE)