Heatmap in R with raw values

Question

I have this dataframe:

df <- data.frame(PatientID = c("3454","345","5","348","567","79"),
                 clas1 = c(1, 0, 5, NA, NA, 4),
                 clas2 = c(4, 1, 0, 3, 1, 0),
                 clas3 = c(1, NA, 0, 5, 5, 5), stringsAsFactors = F)

I would like to create a heatmap, with patient ID in the x axis and clas1, clas2 and clas3 in the y axis. The values represented in the heat map would be the raw value of each "clas". Here I post a drawing of what I would like

I apologise because I don't have available more colours to represent this, but this is only an example and any colour scale could be used. An important thing is that I would like to distinguish between zeros and NAs so ideally NAs have their own colour or appear in white (empty).

I hope this is understandable enough.

But any questions just ask

Many thanks!

Answer 1

Preparing the data

I'll give 4 options, in all four you need to assign the rownames and remove the id column. I.e.:

df <- data.frame(PatientID = c("3454","345","5","348","567","79"),
                 clas1 = c(1, 0, 5, NA, NA, 4),
                 clas2 = c(4, 1, 0, 3, 1, 0),
                 clas3 = c(1, NA, 0, 5, 5, 5), stringsAsFactors = F)
rownames(df) <- df$PatientID
df$PatientID <- NULL
df

The output is:

> df
     clas1 clas2 clas3
3454     1     4     1
345      0     1    NA
5        5     0     0
348     NA     3     5
567     NA     1     5
79       4     0     5

Base R

With base R (decent output):

heatmap(as.matrix(df))

gplots

With gplots (a bit ugly, but many more parameters to control):

library(gplots)
heatmap.2(as.matrix(df))

heatmaply

With heatmaply you have nicer defaults to use for the dendrograms (it also organizes them in a more "optimal" way).

You can learn more about the package here.

Static

Static heatmap with heatmaply (better defaults, IMHO)

library(heatmaply)
ggheatmap(df)

Now with colored dendrograms

library(heatmaply)
ggheatmap(df, k_row = 3, k_col = 2)

With no dendrogram:

library(heatmaply)
ggheatmap(df, dendrogram = F)

Interactive

Interactive heatmap with heatmaply (hover tooltip, and the ability to zoom - it's interactive!):

library(heatmaply)
heatmaply(df)

And anything you can do with the static ggheatmap you can also do with the interactive heatmaply version.

Answer 2

df <- data.frame(PatientID = c("3454","345","5","348","567","79"),
                 clas1 = c(1, 0, 5, NA, NA, 4),
                 clas2 = c(4, 1, 0, 3, 1, 0),
                 clas3 = c(1, NA, 0, 5, 5, 5), stringsAsFactors = F)
library(tidyverse)
df %>% pivot_longer(!PatientID) %>%
  ggplot(aes(x= PatientID, y = name, fill = value)) +
  geom_tile()

^{Created on 2021-05-25 by the reprex package (v2.0.0)}

Answer 3

Here is a base R option with ``heatmap`

heatmap(t(`row.names<-`(as.matrix(df[-1]), df$PatientID)))

# Which is like
# x <- as.matrix(df[-1]
# row.names(x) <- df$PatientID
# heatmap(t(x))

Answer 4

Here is another option:

df <- data.frame(PatientID = c("3454","345","5","348","567","79"),
                 clas1 = c(1, 0, 5, NA, NA, 4),
                 clas2 = c(4, 1, 0, 3, 1, 0),
                 clas3 = c(1, NA, 0, 5, 5, 5), stringsAsFactors = F)


# named vector for heatmap
cols <-  c("0" = "white",
           "1" = "green", 
           "2" = "orange", 
           "3" = "yellow", 
           "4" = "pink",
           "5" = "black",
           "99" = "grey")
labels_legend <- c("0" = "0",
                   "1" = "1", 
                   "2" = "2", 
                   "3" = "3", 
                   "4" = "4", 
                   "5" = "5",
                   "99" = "NA")

df1 <- df %>% 
  pivot_longer(
    cols = starts_with("clas"),
    names_to = "names",
    values_to = "values"
  ) %>% 
  mutate(PatientID = factor(PatientID, levels = c("3454", "345", "5", "348", "567", "79")))

ggplot(
  df1, 
  aes(factor(PatientID),  factor(names))) +
  geom_tile(aes(fill= factor(values))) +
  # geom_text(aes(label = values), size = 5, color = "black") + # text in tiles
  scale_fill_manual(
    values = cols, 
    breaks = c("0", "1", "2", "3", "4", "5", "99"),
    labels = labels_legend,
    aesthetics = c("colour", "fill"),
    drop = FALSE
  ) +
  scale_y_discrete(limits=rev) +
  coord_equal() +
  theme(line = element_blank(),
        title = element_blank()) +
  theme(legend.direction = "horizontal", legend.position = "bottom")