https://github.com/romunov/peep
Fit your oversized data.frame to your console width.
https://github.com/romunov/peep
dataframe geneexpression printing r
Last synced: 2 months ago
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Fit your oversized data.frame to your console width.
- Host: GitHub
- URL: https://github.com/romunov/peep
- Owner: romunov
- Created: 2020-06-07T18:02:23.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-07-15T16:14:32.000Z (almost 5 years ago)
- Last Synced: 2025-03-28T02:24:38.629Z (3 months ago)
- Topics: dataframe, geneexpression, printing, r
- Language: R
- Homepage:
- Size: 33.2 KB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
peep
========================
R's default `head` or `tail` functions print 6 or so rows and all columns. When you have a dataset that has a rather large number of columns, printing can be very poor, spilling over several rows.
The default output would look like
```
> dim(xy)
[1] 43 205
> head(xy)
Sample SLC25A5 MEOX1 CD4 HFE GABRA3 RNH1 VIM MYOC
1 sample 1 169.28930 0.08670971 18.975543 14.149516 0.10174355 5.021980 1674.99418 0.2268739
2 sample 2 122.55490 0.11898911 16.644021 5.116629 0.06980979 4.246349 610.15708 0.9339964
3 sample 3 13.49505 0.39190042 7.006248 8.686389 0.61902692 1.242957 88.91675 11.1807812
4 sample 4 111.84583 0.07831660 8.329725 2.129984 0.34920184 8.478207 194.47382 0.0000000
CAPG ZIC2 EPHA3 ELN NTN1 ABCC9 CYBRD1 NTN4 NUAK1 SLC25A3
1 48.951242 0.9216751 5.97980198 3.591096 4.5935819 12.916405 45.980617 10.402553 6.992939 81.73932
2 10.396297 1.0434491 19.52954610 4.078562 5.2744688 40.005469 17.813941 15.819005 9.638139 60.31633
3 2.468217 3.6529801 2.96681949 5.578765 0.5051865 6.682470 1.563846 1.976812 2.269706 11.34410
4 24.162310 3.4463885 0.07879854 3.225239 2.1506768 1.343375 20.593887 4.886979 3.763131 56.44569
...
```
spilling columns over several lines with no end in sight for data with large number of colums (think expressions in bioinformatics).
It came down to typing `xy[1:5, 1:5]` for the rest of my life or develop a function that would make this easier. Enter `peep`. It prints a few first and last rows and columns. If any columns or rows have been omitted, it adds a horizontal or vertical delimiter of dots to indicate that there's something there.
```
> peep(xy)
Sample SLC25A5 MEOX1 CD4 HFE GABRA3 MMP12 SPON1 MSMB CCL4 CCL3
01: sample 1 169.3 0.08671 18.98 14.15 0.1017 · 5.77 45.49 8.803 77.19 76.08
02: sample 2 122.6 0.119 16.64 5.117 0.06981 · 114.9 274.7 0.2449 44.92 41.04
03: sample 3 13.5 0.3919 7.006 8.686 0.619 · 4.861 2.803 278 9.299 5.599
04: sample 4 111.8 0.07832 8.33 2.13 0.3492 · 146.8 560.5 0 25.22 16.66
05: sample 5 92.04 0 0.9135 0.8531 0.8672 · 91.63 8.617 4.848 8.899 6.03
06: sample 6 63.44 0.3779 4.487 11.16 4.573 · 273.6 7.65 20.03 15.84 9.727
· · · · · · · · · · · ·
38: sample 38 119.9 0.06032 2.194 8.856 0 · 1.158 4.308 0 8.464 19.14
39: sample 39 83.36 0 5.265 1.505 0 · 7.512 225.4 0 17.25 16.83
40: sample 40 100.1 0 4.783 1.692 0 · 88.81 18.54 0 55.66 5.438
41: sample 41 77.02 0.01632 14.92 3.389 0.01915 · 0 68.71 0 18.79 11.5
42: sample 42 39.37 0.1706 4.553 4.284 0.2891 · 6.476 20.21 8.893 21.19 9.978
43: sample 43 36.44 0 1.064 4.322 0.4157 · 0.544 5.627 0 5.444 2.933
```
This works has been inspired by [`data.table`](https://github.com/Rdatatable/data.table) and [pandas](https://github.com/pandas-dev/pandas), a package for working with DataFrames in Python.
# Installation
To install from GitHub, try using package `remotes`
```
remotes::install_github("romunov/peep")
```