Last updated on 2022-04-08 01:49:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.0 | 17.94 | 315.29 | 333.23 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.0 | 15.36 | 231.42 | 246.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.6.0 | 389.63 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.6.0 | 369.14 | OK | |||
| r-devel-windows-x86_64-new-UL | 1.6.0 | 116.00 | 325.00 | 441.00 | OK | |
| r-patched-linux-x86_64 | 1.6.0 | 23.13 | 294.16 | 317.29 | OK | |
| r-release-linux-x86_64 | 1.6.0 | 13.26 | 284.34 | 297.60 | OK | |
| r-release-macos-arm64 | 1.6.0 | OK | ||||
| r-release-macos-x86_64 | 1.6.0 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.6.0 | 43.00 | 324.00 | 367.00 | OK | |
| r-oldrel-macos-x86_64 | 1.6.0 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.6.0 | 43.00 | 198.00 | 241.00 | ERROR |
Version: 1.6.0
Check: for unstated dependencies in examples
Result: WARN
Warning: parse error in file 'lines':
19: unexpected '>'
388:
389: tidyHeatmap::N52 |>
^
Flavor: r-oldrel-macos-x86_64
Version: 1.6.0
Check: examples
Result: ERROR
Running examples in ‘tidyHeatmap-Ex.R’ failed
The error most likely occurred in:
> ### Name: wrap_heatmap
> ### Title: Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch
> ### Aliases: wrap_heatmap wrap_heatmap,InputHeatmap-method
>
> ### ** Examples
>
>
>
> tidyHeatmap::N52 |>
Error: unexpected '>' in "tidyHeatmap::N52 |>"
Execution halted
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Attaching package: 'tidyHeatmap'
The following object is masked from 'package:stats':
heatmap
>
> test_check("tidyHeatmap")
Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") :
tests.R:47:20: unexpected '>'
46: .value = `read count normalised log`
47: ) |>
^
Calls: test_check ... doTryCatch -> lapply -> FUN -> source_file -> parse
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.6.0
Check: for unstated dependencies in vignettes
Result: NOTE
Warning: parse error in file '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/tidyHeatmap.Rcheck/tidyHeatmap/doc/introduction.R':
20:17: unexpected '>'
19: mtcars_tidy <-
20: mtcars |>
^
Flavor: r-oldrel-macos-x86_64
Version: 1.6.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
## Citation
Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472
Please have a look also to
- [tidygate](https://github.com/stemangiola/tidygate/) for adding custom gate information to your tibble
- [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) for tidy manipulation of Seurat objects
- [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy manipulation of Seurat objects
- [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy high-level data analysis and manipulation
- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/) for heatmaps produced with tidy principles
website: [stemangiola.github.io/tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/)
`tidyHeatmap` is a package that introduces tidy principles to the creation of information-rich heatmaps.
This package uses [ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) as graphical engine.
**Advantages:**
- Modular annotation with just specifying column names
- Custom grouping of rows is easy to specify providing a grouped tbl.
For example `df |> group_by(...)`
- Labels size adjusted by row and column total number
- Default use of Brewer and Viridis palettes
## Functions/utilities available
Function | Description
------------ | -------------
`heatmap` | Plots base heatmap
`add_tile` | Adds tile annotation to the heatmap
`add_point` | Adds point annotation to the heatmap
`add_bar` | Adds bar annotation to the heatmap
`add_line` | Adds line annotation to the heatmap
`layer_point` | Adds layer of symbols on top of the heatmap
`layer_square` | Adds layer of symbols on top of the heatmap
`layer_diamond` | Adds layer of symbols on top of the heatmap
`layer_arrow_up` | Adds layer of symbols on top of the heatmap
`layer_arrow_down` | Add layer of symbols on top of the heatmap
`split_rows` | Splits the rows based on the dendogram
`split_columns` | Splits the columns based on the dendogram
`save_pdf` | Saves the PDF of the heatmap
## Installation
To install the most up-to-date version
```r
devtools::install_github("stemangiola/tidyHeatmap")
```
To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage)
```r
install.packages("tidyHeatmap")
```
## Contribution
If you want to contribute to the software, report issues or problems with the software or seek support please open an issue [here](https://github.com/stemangiola/tidyHeatmap/issues)
## Input data frame
The heatmaps visualise a multi-element, multi-feature dataset, annotated with independent variables. Each observation is a element-feature pair (e.g., person-physical characteristics).
element | feature | value | independent_variables
------------ | ------------- | ------------- | -------------
`chr` or `fctr` | `chr` or `fctr` | `numeric` | ...
Let's transform the mtcars dataset into a tidy "element-feature-independent variables" data frame. Where the independent variables in this case are 'hp' and 'vs'.
Quitting from lines 85-96 (./../man/fragments/intro.Rmd)
Quitting from lines 48-52 (./../man/fragments/intro.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
<text>:2:17: unexpected '>'
1: mtcars_tidy <-
2: mtcars |>
^
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.6.0
Check: for unstated dependencies in examples
Result: WARN
Warning: parse error in file 'lines':
19: unexpected '>'
389:
390: tidyHeatmap::N52 |>
^
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: for unstated dependencies in ‘tests’
Result: WARN
Warning: parse error in file 'testthat/tests.R':
47:20: unexpected '>'
46: .value = `read count normalised log`
47: ) |>
^
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: tests
Result: ERROR
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(tidyHeatmap)
========================================
tidyHeatmap version 1.6.0
If you use tidyHeatmap in published research, please cite:
1) Mangiola et al. tidyHeatmap: an R package for modular heatmap production
based on tidy principles. JOSS 2020.
2) Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyHeatmap))
========================================
Attaching package: 'tidyHeatmap'
The following object is masked from 'package:stats':
heatmap
>
> test_check("tidyHeatmap")
Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") :
tests.R:47:20: unexpected '>'
46: .value = `read count normalised log`
47: ) |>
^
Calls: test_check ... doTryCatch -> lapply -> FUN -> source_file -> parse
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: for unstated dependencies in vignettes
Result: NOTE
Warning: parse error in file 'd:/RCompile/CRANpkg/lib/4.0/tidyHeatmap/doc/introduction.R':
/RCompile/CRANpkg/lib/4.0/tidyHeatmap/doc/introduction.R:20:17: unexpected '>'
19: mtcars_tidy <-
20: mtcars |>
^
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
## Citation
Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472
Please have a look also to
- [tidygate](https://github.com/stemangiola/tidygate/) for adding custom gate information to your tibble
- [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) for tidy manipulation of Seurat objects
- [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy manipulation of Seurat objects
- [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy high-level data analysis and manipulation
- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/) for heatmaps produced with tidy principles
website: [stemangiola.github.io/tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/)
`tidyHeatmap` is a package that introduces tidy principles to the creation of information-rich heatmaps.
This package uses [ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) as graphical engine.
**Advantages:**
- Modular annotation with just specifying column names
- Custom grouping of rows is easy to specify providing a grouped tbl.
For example `df |> group_by(...)`
- Labels size adjusted by row and column total number
- Default use of Brewer and Viridis palettes
## Functions/utilities available
Function | Description
------------ | -------------
`heatmap` | Plots base heatmap
`add_tile` | Adds tile annotation to the heatmap
`add_point` | Adds point annotation to the heatmap
`add_bar` | Adds bar annotation to the heatmap
`add_line` | Adds line annotation to the heatmap
`layer_point` | Adds layer of symbols on top of the heatmap
`layer_square` | Adds layer of symbols on top of the heatmap
`layer_diamond` | Adds layer of symbols on top of the heatmap
`layer_arrow_up` | Adds layer of symbols on top of the heatmap
`layer_arrow_down` | Add layer of symbols on top of the heatmap
`split_rows` | Splits the rows based on the dendogram
`split_columns` | Splits the columns based on the dendogram
`save_pdf` | Saves the PDF of the heatmap
## Installation
To install the most up-to-date version
```r
devtools::install_github("stemangiola/tidyHeatmap")
```
To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage)
```r
install.packages("tidyHeatmap")
```
## Contribution
If you want to contribute to the software, report issues or problems with the software or seek support please open an issue [here](https://github.com/stemangiola/tidyHeatmap/issues)
## Input data frame
The heatmaps visualise a multi-element, multi-feature dataset, annotated with independent variables. Each observation is a element-feature pair (e.g., person-physical characteristics).
element | feature | value | independent_variables
------------ | ------------- | ------------- | -------------
`chr` or `fctr` | `chr` or `fctr` | `numeric` | ...
Let's transform the mtcars dataset into a tidy "element-feature-independent variables" data frame. Where the independent variables in this case are 'hp' and 'vs'.
Quitting from lines 85-96 (./../man/fragments/intro.Rmd)
Quitting from lines 48-52 (./../man/fragments/intro.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
<text>:2:17: unexpected '>'
1: mtcars_tidy <-
2: mtcars |>
^
--- failed re-building 'introduction.Rmd'
SUMMARY: processing the following file failed:
'introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64