From 9d3e4591406f8056f16f812d52a839ace7323bbc Mon Sep 17 00:00:00 2001 From: Niels van der Velden Date: Thu, 6 Jun 2024 14:00:15 -0300 Subject: [PATCH] Update documentation and examples --- DESCRIPTION | 11 +- R/transcript.R | 2 +- README.md | 6 +- docs/articles/BLASTP.html | 6 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/Examples.html | 33 ++- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/LoadFastaFiles.html | 4 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/LoadGFF.html | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/LoadGenBankFiles.html | 6 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/MUMMER.html | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/articles/geneviewer.html | 223 ++++++++---------- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/index.html | 8 +- docs/pkgdown.yml | 2 +- docs/reference/BRCA1_splice_variants.html | 4 +- docs/reference/GC_align.html | 2 +- docs/reference/GC_annotation.html | 2 +- docs/reference/GC_chart.html | 14 +- docs/reference/GC_cluster.html | 2 +- docs/reference/GC_clusterFooter.html | 4 +- docs/reference/GC_clusterLabel.html | 6 +- docs/reference/GC_clusterTitle.html | 4 +- docs/reference/GC_color.html | 6 +- docs/reference/GC_coordinates.html | 4 +- docs/reference/GC_genes.html | 4 +- docs/reference/GC_grid.html | 4 +- docs/reference/GC_labels.html | 6 +- docs/reference/GC_legend.html | 2 +- docs/reference/GC_links.html | 6 +- docs/reference/GC_scale.html | 2 +- docs/reference/GC_scaleBar.html | 4 +- docs/reference/GC_sequence.html | 4 +- docs/reference/GC_title.html | 4 +- docs/reference/GC_tooltip.html | 2 +- docs/reference/GC_trackMouse.html | 2 +- docs/reference/GC_transcript.html | 81 ++++--- .../figures/BRCA1_splice_variants.png | Bin 0 -> 136591 bytes docs/reference/get_introns.html | 117 +++++++++ docs/reference/index.html | 5 + .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- .../lib/geneviewer-0.1.7/geneviewer.js | 2 +- docs/search.json | 2 +- docs/sitemap.xml | 3 + man/figures/BRCA1_splice_variants.png | Bin 0 -> 136591 bytes man/get_introns.Rd | 2 +- vignettes/geneviewer.Rmd | 34 ++- 74 files changed, 420 insertions(+), 281 deletions(-) create mode 100644 docs/reference/figures/BRCA1_splice_variants.png create mode 100644 docs/reference/get_introns.html create mode 100644 man/figures/BRCA1_splice_variants.png diff --git a/DESCRIPTION b/DESCRIPTION index 0489bf0..0934ede 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,11 +4,12 @@ Title: Gene Cluster Visualizations in R Version: 0.1.7 Author: Niels van der Velden Maintainer: Niels van der Velden -Description: 'geneviewer' is an R package for plotting gene clusters. - It imports data from GenBank, FASTA, and GFF files, performs BlastP - and MUMmer alignments, and displays results on gene arrow maps. - The package offers extensive customization options, including - legends, labels, annotations, scales, colors, tooltips, and more. +Description: 'geneviewer' is an R package for plotting gene clusters and + transcripts.It imports data from GenBank, FASTA, and GFF files, + performs BlastP and MUMmer alignments, and displays results on + gene arrow maps. The package offers extensive customization + options, including legends, labels, annotations, scales, + colors, tooltips, and more. License: MIT + file LICENSE Encoding: UTF-8 LazyData: true diff --git a/R/transcript.R b/R/transcript.R index 5ff156c..eb7cc20 100644 --- a/R/transcript.R +++ b/R/transcript.R @@ -13,7 +13,7 @@ #' #' @return A dataframe with the original exons and the calculated introns, sorted #' by transcript and start position. Each row includes the `start`, `end`, -#' `type` (exon or intron), `transcript`, and `strand` for each segment. +#' `type` (exon, UTR or intron), `transcript`, and `strand` for each segment. #' #' @importFrom dplyr mutate filter group_by arrange lead select bind_rows #' @importFrom rlang .data diff --git a/README.md b/README.md index 97c6e12..ae3a939 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ## geneviewer -**geneviewer** is an R package for plotting gene clusters. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html). +**geneviewer** is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html). ## Installation @@ -54,6 +54,10 @@ For additional examples and the corresponding code to create the plots, please v
+ + +
+
diff --git a/docs/articles/BLASTP.html b/docs/articles/BLASTP.html index 0fa23eb..75ed3fb 100644 --- a/docs/articles/BLASTP.html +++ b/docs/articles/BLASTP.html @@ -382,7 +382,7 @@

Run BlastPGC_clusterLabel() %>% GC_legend(FALSE)
- +

Color by gene function @@ -475,7 +475,7 @@

Color by gene functionGC_clusterLabel() %>% GC_legend(TRUE)

-

Alternatively, the GC_links() function allows for highlighting +

Alternatively, the GC_links() function allows for highlighting connections between specific genes by utilizing the value1 and value2 parameters. To gain insights into the cluster sizes, we can adjust the axis_type to range. For additional styling and coloring options, refer @@ -498,7 +498,7 @@

Color by gene functionGC_clusterLabel() %>% GC_legend(TRUE)
- + diff --git a/docs/articles/BLASTP_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/BLASTP_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/BLASTP_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/BLASTP_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/BLASTP_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/BLASTP_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/BLASTP_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/BLASTP_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/BLASTP_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/BLASTP_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/BLASTP_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/BLASTP_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/BLASTP_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/BLASTP_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/BLASTP_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/BLASTP_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/Examples.html b/docs/articles/Examples.html index 4261793..8d2cee1 100644 --- a/docs/articles/Examples.html +++ b/docs/articles/Examples.html @@ -138,7 +138,7 @@

) %>% GC_legend(FALSE)
- +

Omphalotin gene clusters @@ -166,7 +166,7 @@

Omphalotin gene clusters )


- +

@@ -234,22 +234,20 @@

GC_cluster(prevent_gene_overlap = TRUE, overlap_spacing=20)


- +

BRCA1 splice variants

-
-
+
Click to see the code 
-GC_chart(BRCA1_splice_variants, 
-         start = "start", 
-         end = "end", 
-         strand = "strand", 
-         transcript = "ensembl_transcript_id", 
-         type = "type",
-         height = "600px") %>% 
+GC_chart(BRCA1_splice_variants, height = "600px") %>%
+  GC_transcript(
+    transcript = "ensembl_transcript_id", 
+    strand = "strand", 
+    type = "type",
+  ) %>%
   GC_clusterTitle(
     title = unique(BRCA1_splice_variants$ensembl_transcript_id),
     titleFont = list(
@@ -260,7 +258,8 @@ 
BRCA1 splice variants    title = c("0.8%", "0.1%", "0.07%", "0.02%", "0.01%"),
     align = "center"
   )
-
+
+

@@ -312,7 +311,7 @@

GC_color(customColors = colors)


- +

@@ -338,8 +337,7 @@

) %>% GC_clusterLabel()

-
-
+
Click to see the code 
 library(dplyr)
@@ -357,7 +355,8 @@ 

            ) %>%
   GC_clusterLabel() %>%
   GC_legend(FALSE)
-
+
+ diff --git a/docs/articles/Examples_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/Examples_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/Examples_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/Examples_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/Examples_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/Examples_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/Examples_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/Examples_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/Examples_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/Examples_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/Examples_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/Examples_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/Examples_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js b/docs/articles/Examples_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js index cf6ceb5..ccddce8 100644 --- a/docs/articles/Examples_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js +++ b/docs/articles/Examples_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js @@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) { const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons); const yOffset = d.direction === 'forward' ? -height : +height; const rotation = this.reverse - ? (d.direction === 'forward' ? 180 : 0) + ? (d.direction === 'reverse' ? 180 : 0) : (d.direction === 'forward' ? 0 : 180); return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`; }) diff --git a/docs/articles/LoadFastaFiles.html b/docs/articles/LoadFastaFiles.html index 3ccaae0..3cb49a2 100644 --- a/docs/articles/LoadFastaFiles.html +++ b/docs/articles/LoadFastaFiles.html @@ -269,7 +269,7 @@

Cluster Visualization GC_clusterLabel(unique(fasta_df$cluster)) chart
- +

Uniprot Keywords @@ -488,7 +488,7 @@

Uniprot Keywords ) chart

-

For further customization options like setting a title, altering the +

For further customization options like setting a title, altering the colors adding gene links and much more see Get Started and Examples.