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fix: vignette and README examples synchronized
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@m-jahn
m-jahn committed Apr 16, 2024
1 parent 16b19e9 commit 85d8ac0
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7 changes: 6 additions & 1 deletion README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,15 @@ knitr::opts_chunk$set(
<img src = "man/figures/ggcoverage.png" align = "right" width = "200"/>

[![CRAN](https://www.r-pkg.org/badges/version/ggcoverage?color=orange)](https://cran.r-project.org/package=ggcoverage)
[![R-CMD-check](https://github.com/showteeth/ggcoverage/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/showteeth/ggcoverage/actions/workflows/R-CMD-check.yaml)
![GitHub issues](https://img.shields.io/github/issues/showteeth/ggcoverage)
![GitHub last commit](https://img.shields.io/github/last-commit/showteeth/ggcoverage)
![License](https://img.shields.io/badge/license-MIT-green)
[![CODE_SIZE](https://img.shields.io/github/languages/code-size/showteeth/ggcoverage.svg)](https://github.com/showteeth/ggcoverage)

## Introduction
The goal of `ggcoverage` is simplify the process of visualizing omics coverage. It contains three main parts:

The goal of `ggcoverage` is simplify the process of visualizing omics coverage. It contains three main parts:

* **Load the data**: `ggcoverage` can load BAM, BigWig (.bw), BedGraph, txt/xlsx files from various omics data, including WGS, RNA-seq, ChIP-seq, ATAC-seq, proteomics, et al.
* **Create omics coverage plot**
Expand Down Expand Up @@ -67,6 +71,7 @@ library("ggpattern")
```

## Manual

`ggcoverage` provides two [vignettes](https://showteeth.github.io/ggcoverage/):

* **detailed manual**: step-by-step usage
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83 changes: 46 additions & 37 deletions README.md
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Expand Up @@ -6,6 +6,11 @@
<img src = "man/figures/ggcoverage.png" align = "right" width = "200"/>

[![CRAN](https://www.r-pkg.org/badges/version/ggcoverage?color=orange)](https://cran.r-project.org/package=ggcoverage)
[![R-CMD-check](https://github.com/showteeth/ggcoverage/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/showteeth/ggcoverage/actions/workflows/R-CMD-check.yaml)
![GitHub
issues](https://img.shields.io/github/issues/showteeth/ggcoverage)
![GitHub last
commit](https://img.shields.io/github/last-commit/showteeth/ggcoverage)
![License](https://img.shields.io/badge/license-MIT-green)
[![CODE_SIZE](https://img.shields.io/github/languages/code-size/showteeth/ggcoverage.svg)](https://github.com/showteeth/ggcoverage)

Expand Down Expand Up @@ -117,13 +122,13 @@ track_df <- LoadTrackFile(
)
# check data
head(track_df)
#> seqnames start end score Type Group
#> 1 chr14 21675306 21675950 0 KO_rep1 KO
#> 2 chr14 21675951 21676000 1 KO_rep1 KO
#> 3 chr14 21676001 21676100 2 KO_rep1 KO
#> 4 chr14 21676101 21676150 1 KO_rep1 KO
#> 5 chr14 21676151 21677100 0 KO_rep1 KO
#> 6 chr14 21677101 21677200 2 KO_rep1 KO
#> seqnames start end width strand score Type Group
#> 1 chr14 21675306 21675950 645 * 0 KO_rep1 KO
#> 2 chr14 21675951 21676000 50 * 1 KO_rep1 KO
#> 3 chr14 21676001 21676100 100 * 2 KO_rep1 KO
#> 4 chr14 21676101 21676150 50 * 1 KO_rep1 KO
#> 5 chr14 21676151 21677100 950 * 0 KO_rep1 KO
#> 6 chr14 21677101 21677200 100 * 2 KO_rep1 KO
```

Prepare mark region:
Expand Down Expand Up @@ -414,20 +419,20 @@ track_file <-
track_df <- LoadTrackFile(track.file = track_file,
format = "bw",
region = "4:1-160000000")
#> Sample without metadata!
#> No metadata provided, returning coverage as is.

# add chr prefix
track_df$seqnames <- paste0("chr", track_df$seqnames)

# check data
head(track_df)
#> seqnames start end score Type Group
#> 1 chr4 1 50000 197 SRR054616.bw SRR054616.bw
#> 2 chr4 50001 100000 598 SRR054616.bw SRR054616.bw
#> 3 chr4 100001 150000 287 SRR054616.bw SRR054616.bw
#> 4 chr4 150001 200000 179 SRR054616.bw SRR054616.bw
#> 5 chr4 200001 250000 282 SRR054616.bw SRR054616.bw
#> 6 chr4 250001 300000 212 SRR054616.bw SRR054616.bw
#> seqnames start end width strand score Type Group
#> 1 chr4 1 50000 50000 * 197 SRR054616.bw SRR054616.bw
#> 2 chr4 50001 100000 50000 * 598 SRR054616.bw SRR054616.bw
#> 3 chr4 100001 150000 50000 * 287 SRR054616.bw SRR054616.bw
#> 4 chr4 150001 200000 50000 * 179 SRR054616.bw SRR054616.bw
#> 5 chr4 200001 250000 50000 * 282 SRR054616.bw SRR054616.bw
#> 6 chr4 250001 300000 50000 * 212 SRR054616.bw SRR054616.bw
```

##### Basic coverage
Expand Down Expand Up @@ -514,15 +519,18 @@ track_df <- LoadTrackFile(
single.nuc = TRUE,
single.nuc.region = "chr4:62474235-62474295"
)
#> No 'region' specified; extracting coverage for an example range
#> (<=100,000 bases, first annotated sequence)
#> Coverage extracted from sequence/chromosome: chr10

head(track_df)
#> seqnames start end score Type Group
#> 1 chr4 62474235 62474236 5 tumorA tumorA
#> 2 chr4 62474236 62474237 5 tumorA tumorA
#> 3 chr4 62474237 62474238 5 tumorA tumorA
#> 4 chr4 62474238 62474239 6 tumorA tumorA
#> 5 chr4 62474239 62474240 6 tumorA tumorA
#> 6 chr4 62474240 62474241 6 tumorA tumorA
#> seqnames start end width strand score Type Group
#> 1 chr4 62474235 62474236 1 * 5 tumorA tumorA
#> 2 chr4 62474236 62474237 1 * 5 tumorA tumorA
#> 3 chr4 62474237 62474238 1 * 5 tumorA tumorA
#> 4 chr4 62474238 62474239 1 * 6 tumorA tumorA
#> 5 chr4 62474239 62474240 1 * 6 tumorA tumorA
#> 6 chr4 62474240 62474241 1 * 6 tumorA tumorA
```

#### Default color scheme
Expand Down Expand Up @@ -566,6 +574,7 @@ graphics::mtext(
<img src="man/figures/README-base_color_scheme-1.png" width="100%" style="display: block; margin: auto;" />

``` r

# reset par default
graphics::par(opar)
```
Expand Down Expand Up @@ -734,13 +743,13 @@ track_df <- LoadTrackFile(

# check data
head(track_df)
#> seqnames start end score Type Group
#> 1 chr18 76820285 76820400 219.658005 MCF7_ER_1 IP
#> 2 chr18 76820401 76820700 0.000000 MCF7_ER_1 IP
#> 3 chr18 76820701 76821000 439.316010 MCF7_ER_1 IP
#> 4 chr18 76821001 76821300 219.658005 MCF7_ER_1 IP
#> 5 chr18 76821301 76821600 0.000000 MCF7_ER_1 IP
#> 6 chr18 76821601 76821900 219.658005 MCF7_ER_1 IP
#> seqnames start end width strand score Type Group
#> 1 chr18 76820285 76820400 116 * 219.658005 MCF7_ER_1 IP
#> 2 chr18 76820401 76820700 300 * 0.000000 MCF7_ER_1 IP
#> 3 chr18 76820701 76821000 300 * 439.316010 MCF7_ER_1 IP
#> 4 chr18 76821001 76821300 300 * 219.658005 MCF7_ER_1 IP
#> 5 chr18 76821301 76821600 300 * 0.000000 MCF7_ER_1 IP
#> 6 chr18 76821601 76821900 300 * 219.658005 MCF7_ER_1 IP
```

Prepare mark region:
Expand Down Expand Up @@ -817,19 +826,19 @@ track_df <- LoadTrackFile(
region = "chr2L:8050000-8300000",
extend = 0
)
#> Sample without metadata!
#> No metadata provided, returning coverage as is.

track_df$score <- ifelse(track_df$score < 0, 0, track_df$score)

# check the data
head(track_df)
#> seqnames start end score Type Group
#> 1 chr2L 8050000 8050009 1.66490245 H3K36me3.bw H3K36me3.bw
#> 2 chr2L 8050015 8050049 1.59976900 H3K36me3.bw H3K36me3.bw
#> 3 chr2L 8050057 8050091 1.60730922 H3K36me3.bw H3K36me3.bw
#> 4 chr2L 8050097 8050131 1.65555012 H3K36me3.bw H3K36me3.bw
#> 5 chr2L 8050137 8050171 1.71025538 H3K36me3.bw H3K36me3.bw
#> 6 chr2L 8050176 8050210 1.75198197 H3K36me3.bw H3K36me3.bw
#> seqnames start end width strand score Type Group
#> 1 chr2L 8050000 8050009 10 * 1.66490245 H3K36me3.bw H3K36me3.bw
#> 2 chr2L 8050015 8050049 35 * 1.59976900 H3K36me3.bw H3K36me3.bw
#> 3 chr2L 8050057 8050091 35 * 1.60730922 H3K36me3.bw H3K36me3.bw
#> 4 chr2L 8050097 8050131 35 * 1.65555012 H3K36me3.bw H3K36me3.bw
#> 5 chr2L 8050137 8050171 35 * 1.71025538 H3K36me3.bw H3K36me3.bw
#> 6 chr2L 8050176 8050210 35 * 1.75198197 H3K36me3.bw H3K36me3.bw
```

### Load Hi-C data
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