CODEWITHSUNDEEP
rggplot2heatmap
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Reputation: 705

How to plot a heat map by chromosome in R

I have a data table in the following format:

set.seed(1)

dt <- data.table(
chromosome = c(rep(1, 100), 
     rep(2, 100), 
     rep(3, 80)),
mb_from = c(seq(1, 1000, by=10),
      seq(1, 1000, by=10),
      seq(1, 800, by=10)),
mb_to = c(seq(10, 1000, by=10),
    seq(10, 1000, by=10),
    seq(10, 800, by=10)),
score = c(sample(1:10, 100, replace = T),
       sample(1:10, 100, replace = T),
       sample(1:10, 80, replace = T))
)

And I am trying to plot a figure similar (but not identical) to this:

enter image description here

I have tried using ggplot and geom_rect(), but with no luck.

Any help will be greatly appreciated.

Upvotes: 0

Views: 1249

Answers (1)

Paul
Paul

Reputation: 2959

You could try the plotly package, here's a start:

library(dplyr)
library(plotly)
library(RColorBrewer)

dat <- apply(dt,
      1,
      function(x) data.table(chromosome = x["chromosome"], mb = x["mb_from"]:x["mb_to"], score = x["score"])
) %>%
  rbindlist()

plot_ly(dat, x = ~chromosome, y = ~mb, z = ~score, type = "heatmap",
        colors = "RdYlBu", reversescale = T) %>%
  layout(yaxis = list(range = c(1000, 0)))

enter image description here

Upvotes: 1

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