How to make an Oncoprint for a single gene in R?

Question

[Biologist]

Hi,

I have a dataframe with following information.

Sample  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-2Y-A9H7-01 FLT3    DOWN    EXP
TCGA-5C-A9VG-01 FLT3    DOWN    EXP
TCGA-5C-A9VH-01 FLT3    DOWN    EXP
TCGA-5R-AA1C-01 FLT3    DOWN    EXP
TCGA-5R-AA1D-01 FLT3    UP  EXP
TCGA-BC-4072-01 FLT3    UP  EXP
TCGA-BC-A10Q-01 FLT3    DOWN    EXP
TCGA-BC-A10W-01 FLT3    DOWN    EXP
TCGA-BC-A110-01         
TCGA-BC-A5W4-01         
TCGA-BC-A69H-01         
TCGA-BD-A3ER-01         
TCGA-BW-A5NQ-01

I want to make an Oncoprint out of the above data. Annotation on the plot needs to be for DOWN - mRNA down regulation, UP - mRNA Up regulation, Empty places - No Alterations.

Ofcourse I know that I can get the plot from cbioportal, but analysis I have done is different. I want to make this plot in R.

[russhh]

show us some code when you've had a look at the oncoprint functionality in ComplexHeatmap https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html

[Biologist]

Does oncoprint function in ComplexHeatmap give for single gene?

[russhh]

Have you looked at it's docs yet?

[Biologist]

I didn't find any thing with single gene. Could you please show me which one to use.

Answer 1

[Kevin Blighe]

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)

[Biologist]

Thanq very much Kevin