Adding hatches or patterns to ggplot bars

Question

Suppose I want to show in a barplot the gene expression results (logFC) based on RNA-seq and q-PCR analysis. My dataset looks like that:

set.seed(42)

f1 <- expand.grid(
  comp = LETTERS[1:3],
  exp = c("qPCR", "RNA-seq"),
  geneID = paste("Gene", 1:4)
)
f1$logfc <- rnorm(nrow(f1))
f1$SE <- runif(nrow(f1), min=0, max=1.5)

My R command line

p=ggplot(f1, aes(x=geneID, y=logfc, fill= comp,color=exp))+
  geom_bar(stat="identity", position =position_dodge2(preserve="single"))+
  theme(axis.text.x = element_text(angle = 45, vjust = 0.5, hjust=1))```

I have this output:

I want to get any mark patterns or hatches on the bars corresponding to one of the variables (exp or comp) and adding the upper error bars as shown in this plot bellow:

Any help please?

Answer 1

Following the linked answer, it seems quite natural how to extend it to your case. In the example below, I'm using some dummy data structured like the head() data you gave, since the csv link gave me a 404.

library(ggplot2)
library(ggpattern)
#> 
#> Attaching package: 'ggpattern'
#> The following objects are masked from 'package:ggplot2':
#> 
#>     flip_data, flipped_names, gg_dep, has_flipped_aes, remove_missing,
#>     should_stop, waiver

# Setting up some dummy data
set.seed(42)
f1 <- expand.grid(
  comp = LETTERS[1:3],
  exp = c("qPCR", "RNA-seq"),
  geneID = paste("Gene", 1:4)
)
f1$logfc <- rnorm(nrow(f1))

ggplot(f1, aes(x = geneID, y = logfc, fill = comp)) +
  geom_col_pattern(
    aes(pattern = exp),
    colour = "black",
    pattern_fill = "black",
    pattern_angle = 45,
    pattern_density = 0.1,
    pattern_spacing = 0.01,
    position = position_dodge2(preserve = 'single'),
  ) +
  scale_pattern_manual(
    values = c("none", "stripe"),
    guide = guide_legend(override.aes = list(fill = "grey70")) # <- make lighter
  ) +
  scale_fill_discrete(
    guide = guide_legend(override.aes = list(pattern = "none")) # <- hide pattern
  )

^{Created on 2021-04-19 by the reprex package (v1.0.0)}

EDIT: if you want to repeat the hatching in the fill legend, you can make an interaction() and then customise a manual fill scale.

ggplot(f1, aes(x = geneID, y = logfc)) +
  geom_col_pattern(
    aes(pattern = exp,
        fill = interaction(exp, comp)), # <- make this an interaction
    colour = "black",
    pattern_fill = "black",
    pattern_angle = 45,
    pattern_density = 0.1,
    pattern_spacing = 0.01,
    position = position_dodge2(preserve = 'single'),
  ) +
  scale_pattern_manual(
    values = c("none", "stripe"),
    guide = guide_legend(override.aes = list(fill = "grey70")) # <- make lighter
  ) +
  scale_fill_manual(
    # Have 3 colours and repeat each twice
    values = rep(scales::hue_pal()(3), each = 2),
    # Extract the second name after the '.' from the `interaction()` call
    labels = function(x) {
      vapply(strsplit(x, "\\."), `[`, character(1), 2)
    },
    # Repeat the pattern over the guide
    guide = guide_legend(
      override.aes = list(pattern = rep(c("none", "stripe"), 3))
    )
  )

^{Created on 2021-04-19 by the reprex package (v1.0.0)}

EDIT2: Now with errorbars:

library(ggplot2)
library(ggpattern)
set.seed(42)

f1 <- expand.grid(
  comp = LETTERS[1:3],
  exp = c("qPCR", "RNA-seq"),
  geneID = paste("Gene", 1:4)
)
f1$logfc <- rnorm(nrow(f1))
f1$SE <- runif(nrow(f1), min=0, max=1.5)

ggplot(f1, aes(x = geneID, y = logfc)) +
  geom_col_pattern(
    aes(pattern = exp,
        fill = interaction(exp, comp)), # <- make this an interaction
    colour = "black",
    pattern_fill = "black",
    pattern_angle = 45,
    pattern_density = 0.1,
    pattern_spacing = 0.01,
    position = position_dodge2(preserve = 'single'),
  ) +
  geom_errorbar(
    aes(
      ymin = logfc,
      ymax = logfc + sign(logfc) * SE,
      group = interaction(geneID, comp, exp)
    ),
    position = "dodge"
  ) +
  scale_pattern_manual(
    values = c("none", "stripe"),
    guide = guide_legend(override.aes = list(fill = "grey70")) # <- make lighter
  ) +
  scale_fill_manual(
    # Have 3 colours and repeat each twice
    values = rep(scales::hue_pal()(3), each = 2),
    # Extract the second name after the '.' from the `interaction()` call
    labels = function(x) {
      vapply(strsplit(x, "\\."), `[`, character(1), 2)
    },
    # Repeat the pattern over the guide
    guide = guide_legend(
      override.aes = list(pattern = rep(c("none", "stripe"), 3))
    )
  )

^{Created on 2021-04-22 by the reprex package (v1.0.0)}