Adding group notations outside of the plots

Question

I'm trying to add notations for groups outside of ggplot like illustrated in the picture below. I have tried with facet_grid but problems arise when it breaks plots apart from each other so it will not be aligned with the plot that is coming next to it

Code to generate the plot:

df %>%
  pivot_longer(cols=biomarkers) %>%
  left_join(., gene_pct_df, by=c("name" = "biomarkers")) %>%
  mutate(bio_factor = as.numeric(factor(biomarker_groups))) %>% 
  mutate(color_scheme = case_when(
    value == "CC" & bio_factor == 1 ~ "a",
    value == "CC" & bio_factor == 2 ~ "b",
    value == "CC" & bio_factor == 3 ~ "c",
    TRUE ~ "d")) %>%
  ggplot(aes(y=reorder(name, bio_factor))) +
  geom_raster(aes(x=factor(patient), fill=color_scheme,
                  alpha=color_scheme),
              show.legend = F) +
  geom_text(aes(x=factor(patient), label=value), size=3,
            show.legend = F) +
  scale_fill_manual(values = c("#F8766D", "#00BA38" ,"#619CFF", "white"),
                    labels = c("a", "b", "c", "d")) +
  scale_alpha_manual(values = c(0.9, 0.9, 0.9, 0.01),
                     labels = c("a", "b", "c", "d")) +
  theme(axis.title.x=element_blank(),
        axis.ticks.y=element_blank(),
        axis.title.y=element_blank(),
        axis.text.x=element_blank(),
        axis.ticks = element_blank(),
        legend.title = element_blank(),
        plot.margin = unit(c(1,1,1,1), "cm"))

Example data to test the function:

n_pat <- 15
patient <- 1:n_pat
treatment <- sample(c("Drug A", "Drug B"), n_pat, replace=TRUE)
change <- rnorm(n_pat, 0, 20)
biomarkers <- c("T790M","Ex19del","L959R","Ex20Ins","MET","ERBB2","EGFR",
                "EGFR2","PIK3CA","KRAS","CDKN2","RB1","ALK","KIT","MET2",
                "Other")
genes <- matrix(sample(x=c("CC", "AA", "AC"), replace=TRUE, size=n_pat * length(biomarkers)), nrow=n_pat, ncol=length(biomarkers))
biomarker_groups <- c(rep("Baseline", 4), rep("SCNA", 3), rep("SNV", 9))
df <- data.frame(patient, treatment, change, genes)
df <- data.frame(patient, treatment, change, genes)
colnames(df) <- c("patient", "treatment", "change", biomarkers)

genes_df <- df %>%
  select(biomarkers)

pcts <- colSums(genes_df == "CC") / length(df)

gene_pct_df <- data.frame(pcts, biomarker_groups, biomarkers)

user_12258459 · Answer

You can specify facet_wrap with free_y for both scale and space, then adjust the panel spacing in theme():

df %>%
  pivot_longer(cols=biomarkers) %>%
  left_join(., gene_pct_df, by=c("name" = "biomarkers")) %>%
  mutate(bio_factor = as.numeric(factor(biomarker_groups))) %>% 
  mutate(color_scheme = case_when(
    value == "CC" & bio_factor == 1 ~ "a",
    value == "CC" & bio_factor == 2 ~ "b",
    value == "CC" & bio_factor == 3 ~ "c",
    TRUE ~ "d")) %>%
  ggplot(aes(y=reorder(name, bio_factor))) +
  geom_raster(aes(x=factor(patient), fill=color_scheme,
                  alpha=color_scheme),
              show.legend = F) +
  geom_text(aes(x=factor(patient), label=value), size=3,
            show.legend = F) +
  scale_fill_manual(values = c("#F8766D", "#00BA38" ,"#619CFF", "white"),
                    labels = c("a", "b", "c", "d")) +
  scale_alpha_manual(values = c(0.9, 0.9, 0.9, 0.01),
                     labels = c("a", "b", "c", "d")) +
  facet_grid(biomarker_groups ~.,
  switch="y",scales="free_y",space = "free_y") + 

  theme(axis.title.x=element_blank(),
        axis.ticks.y=element_blank(),
        axis.title.y=element_blank(),
        axis.text.x=element_blank(),
        axis.ticks = element_blank(),
        legend.title = element_blank(),
        panel.spacing.y=unit(0,"lines"),
        strip.placement = "outside",
        plot.margin = unit(c(1,1,1,1), "cm"))

Adding group notations outside of the plots

1 Answers