rggplot2heatmapmelt
Sectioning in Heat Map using ggplot
I'm trying to plot a heat map, but I want the heat map in four different vertical sections. The first one shall be for "Proneural", then "Neural", then "Classical" and lastly "Mesenchymal"
A sample of my melted data looks something like this:
dput(tdfdarkmagenta1[1:513,])
"TCGA.02.0011.01", "TCGA.02.0014.01", "TCGA.02.0024.01", "TCGA.02.0026.01",
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"TCGA.08.0522.01", "TCGA.12.0619.01", "TCGA.12.0620.01"), X1 = structure(c(1L,
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1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
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1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L
), .Label = c("Proneural", "Neural", "Classical", "Mesenchymal"
), class = "factor"), variable = c("APOL1", "APOL1", "APOL1",
"APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1",
"APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1",
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"APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1",
"APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1",
"APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1", "APOL1",
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6.297859, 5.036076, 5.580978, 5.374182, 6.098891, 5.228106, 4.514317,
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4.655344)), row.names = c(NA, 513L), class = "data.frame")
Overall the melted data has 4 columns and 11,286 rows. The first column, i.e. the "Row.names" shall contribute to the y-axis of the heat plot, and the third column, i.e. "variable" to contribute to the x-axis but they should be sectioned into four sections depending on the entries in the second column, i.e. "X1".
I'm attaching an image showing the two-section heat plot along the x-axis.
Here the tiny white space separation shows the start of a new section on the x-axis.
My attempt can be found here:
tdfdarkmagentaplot<-ggplot(data=tdfdarkmagenta1, mapping=aes(variable, Row.names , fill= value)) +
geom_tile() + theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())+
scale_fill_distiller(palette = "RdBu")
tdfdarkmagentaplot
I'm also being told complexheatmap() function in R is another approach but don't know how to implement it in my dataframe.
All the suggestions are welcomed.
Solution
Add facet wrap and indicate four columns.
ggplot(df[1:500,], aes(x = variable, y = Row.names, fill = value)) +
geom_tile() +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank(),
axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank()) +
scale_fill_distiller(palette = "RdBu") +
facet_wrap(~X1, ncol = 4)
I attempted to use your data. There were some NA values. The scales don't seem to match what you used. Anyhow, this shows what I believe is your desired column layout.
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