tidyprint is an R package that provides multiple printing styles for SummarizedExperiment objects. You can choose among:
-
SummarizedExperiment (default): Standard R/SummarizedExperiment printing style.
-
tidySummarizedExperiment: Tidyverse-friendly tibble abstraction.
-
plyrxp: Top/bottom row truncation for large datasets.
Depending on your workflow and desired console output, tidyprint makes it easy to switch between these printing styles.
You need the `` package to install from GitHub. If you don’t have it, install via:
install.packages("devtools")
Then install tidyprint from GitHub:
devtools::install_github("tidyomics/tidyprint")
Below is an example demonstrating how to use tidyprint with a sample SummarizedExperiment object.
# Load SummarizedExperiment (install if needed)
if (!requireNamespace("SummarizedExperiment", quietly = TRUE)) {
install.packages("BiocManager")
BiocManager::install("SummarizedExperiment")
}
library(SummarizedExperiment)
library(tidyverse)
library(magrittr)
# Example SummarizedExperiment from the package's built-in example
example("SummarizedExperiment", package = "SummarizedExperiment", ask = FALSE)
# Now load tidyprint
library(tidyprint)
By default, print() on a SummarizedExperiment displays the standard SummarizedExperiment info:
# The default style:
se0 %>% print()
# or equivalently:
se0 %>% print(design = 1)
se0 %>% print(design = "SummarizedExperiment")
Example Output:
class: SummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(0):
colnames(6): A B ... E F
Use the “tidySummarizedExperiment” design to view your data in a tidy-friendly tibble format:
# Tidy SummarizedExperiment print:
se0 %>% print(design = 2)
# or
se0 %>% print(design = "tidySummarizedExperiment")
Example Output:
# A SummarizedExperiment-tibble abstraction: 1,200 × 4
# Features=200 | Samples=6 | Assays=counts
.feature .sample counts Treatment
<chr> <chr> <dbl> <chr>
1 1 A 9.21 ChIP
2 2 A 7.56 ChIP
3 3 A 8.27 ChIP
4 4 A 9.73 ChIP
5 5 A 8.61 ChIP
6 6 A 9.64 ChIP
7 7 A 8.59 ChIP
8 8 A 8.62 ChIP
9 9 A 6.11 ChIP
10 10 A 9.38 ChIP
# ℹ 40 more rows
# ℹ Use `print(n = ...)` to see more rows
colData names(1): Treatment
For a more compact view (top and bottom rows), similar to a plyr/tidyverse style:
se0 %>% print(design = 3)
# or
se0 %>% print(design = "plyrxp")
Example Output:
# A tibble: 10 × 7
.features .samples `` counts `` `` Treatment
<int> <chr> <sep!> <dbl> <sep!> <sep!> <chr>
1 1 A | 9.21 | | ChIP
2 2 A | 7.56 | | ChIP
3 3 A | 8.27 | | ChIP
4 4 A | 9.73 | | ChIP
5 5 A | 8.61 | | ChIP
6 196 F | 9.65 | | Input
7 197 F | 8.29 | | Input
8 198 F | 9.78 | | Input
9 199 F | 9.02 | | Input
10 200 F | 9.01 | | Input
You can also limit the number of displayed rows by setting n_print (or a similar argument in your code):
se0 %>% print(design = "plyrxp", n_print = 5)
Example Output:
# A tibble: 5 × 7
.features .samples `` counts `` `` Treatment
<int> <chr> <sep!> <dbl> <sep!> <sep!> <chr>
1 1 A | 9.21 | | ChIP
2 2 A | 7.56 | | ChIP
3 3 A | 8.27 | | ChIP
4 199 F | 9.02 | | Input
5 200 F | 9.01 | | Input