diff --git a/articles/MotifPeeker.html b/articles/MotifPeeker.html index 69c58c6..6b2124c 100644 --- a/articles/MotifPeeker.html +++ b/articles/MotifPeeker.html @@ -74,7 +74,7 @@

Get started

-

Updated: Oct-21-2024

+

Updated: Oct-24-2024

Overview

@@ -287,9 +287,10 @@

Run MotifPeeker= TRUE ) }

-
## Warning in system2("echo", args = paste0(..., collpase = "")): error in running
-## command
-
## [1] "/tmp/RtmpLtbFDt/MotifPeeker_20241021_155435"
+
## Script run successfully. 
+## Output saved at: /tmp/Rtmpd7DNbg/MotifPeeker_20241024_145550 
+## Time taken: 0.88 mins.
+
## [1] "/tmp/Rtmpd7DNbg/MotifPeeker_20241024_145550"

Required Inputs

diff --git a/articles/docker.html b/articles/docker.html index bdfd14e..a9736d1 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -74,7 +74,7 @@

Docker/Singularity Containers

-

Updated: Oct-21-2024

+

Updated: Oct-24-2024

Installation

diff --git a/articles/examples.html b/articles/examples.html index e58ef3f..ce6cfdd 100644 --- a/articles/examples.html +++ b/articles/examples.html @@ -74,7 +74,7 @@

Example Reports

-

Updated: Oct-21-2024

+

Updated: Oct-24-2024

MotifPeeker-reports is a public archive for interactive HTML reports generated by MotifPeeker, along with the code used to produce them.

diff --git a/articles/troubleshooting.html b/articles/troubleshooting.html index a5ad9cb..63004dc 100644 --- a/articles/troubleshooting.html +++ b/articles/troubleshooting.html @@ -74,7 +74,7 @@

Troubleshooting

-

Updated: Oct-21-2024

+

Updated: Oct-24-2024

This vignette provides troubleshooting tips for common issues encountered when using the MotifPeeker package.

If you encounter an issue that is not covered, please open an issue diff --git a/index.html b/index.html index 1d660d0..a1b9cf4 100644 --- a/index.html +++ b/index.html @@ -67,7 +67,7 @@

License: GPL (>= 3)
R build status

-

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene
Updated: Oct-21-2024

+

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene
Updated: Oct-24-2024

Introduction

diff --git a/news/index.html b/news/index.html index b3f6890..1820281 100644 --- a/news/index.html +++ b/news/index.html @@ -48,6 +48,7 @@

MiscellaneousMove utility functions to ‘utilities.R’.
  • Allow vignettes to run without MEME suite installed.
  • Remove stopper() wrapper around stop().
    • +
  • Use message() for parallel executions

    • diff --git a/pkgdown.yml b/pkgdown.yml index d26d507..9e28eb6 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: articles/examples: examples.html MotifPeeker: MotifPeeker.html troubleshooting: troubleshooting.html -last_built: 2024-10-21T15:52Z +last_built: 2024-10-24T14:53Z urls: reference: https://neurogenomics.github.io/MotifPeeker/reference article: https://neurogenomics.github.io/MotifPeeker/articles diff --git a/reference/MotifPeeker.html b/reference/MotifPeeker.html index e5a8544..f04a1a4 100644 --- a/reference/MotifPeeker.html +++ b/reference/MotifPeeker.html @@ -325,7 +325,7 @@

    Examples quiet = TRUE, verbose = FALSE ) -#> [1] "/tmp/RtmpZzzMHV/MotifPeeker_20241021_155246" +#> [1] "/tmp/RtmpvWobol/MotifPeeker_20241024_145407" # }

    diff --git a/reference/check_ENCODE.html b/reference/check_ENCODE.html index 134e6fa..b9cbe06 100644 --- a/reference/check_ENCODE.html +++ b/reference/check_ENCODE.html @@ -84,7 +84,7 @@

    Examples check_ENCODE("ENCFF920TXI", expect_format = c("bed", "gz")) } #> BFC2 -#> "/github/home/.cache/R/BiocFileCache/10da5b9b0a94_ENCFF920TXI.bed.gz" +#> "/github/home/.cache/R/BiocFileCache/10e06efdaffa_ENCFF920TXI.bed.gz" diff --git a/reference/check_JASPAR.html b/reference/check_JASPAR.html index ac9b4ae..0d071e7 100644 --- a/reference/check_JASPAR.html +++ b/reference/check_JASPAR.html @@ -75,7 +75,7 @@

    Value

    Examples 
    check_JASPAR("MA1930.2")
 #>                                                               BFC3 
-#> "/github/home/.cache/R/BiocFileCache/10da3c7bcc07_MA1930.2.jaspar" 
+#> "/github/home/.cache/R/BiocFileCache/10e01c6f5277_MA1930.2.jaspar"
    diff --git a/reference/find_motifs.html b/reference/find_motifs.html index c97503d..1ec9954 100644 --- a/reference/find_motifs.html +++ b/reference/find_motifs.html @@ -148,7 +148,7 @@

    Examples#> icscore nsites pval type pseudocount bkg best_match_name #> 1 15.22492 54 0.12 PCM 0 0.241, 0.... MA0139.2 #> best_match_altname best_db_name -#> 1 CTCF 5d83a5cf894_JASPAR2024_CORE_non-redundant_pfms_meme.txt +#> 1 CTCF 62a79c3a692_JASPAR2024_CORE_non-redundant_pfms_meme.txt #> best_match_offset best_match_pval best_match_eval best_match_qval #> 1 2 3.33e-13 7.81e-10 1.56e-09 #> best_match_strand best_match_motif tomtom @@ -162,7 +162,7 @@

    Examples#> pval type pseudocount bkg best_match_name best_match_altname #> 1 0.5 PCM 0 0.241, 0.... MA1931.1 ELK1::HOXA1 #> best_db_name best_match_offset -#> 1 5d83a5cf894_JASPAR2024_CORE_non-redundant_pfms_meme.txt 3 +#> 1 62a79c3a692_JASPAR2024_CORE_non-redundant_pfms_meme.txt 3 #> best_match_pval best_match_eval best_match_qval best_match_strand #> 1 1.55e-05 0.0365 0.0725 + #> best_match_motif tomtom diff --git a/reference/get_JASPARCORE.html b/reference/get_JASPARCORE.html index ae37a62..0e1a729 100644 --- a/reference/get_JASPARCORE.html +++ b/reference/get_JASPARCORE.html @@ -71,7 +71,7 @@

    Value

    Examples

    get_JASPARCORE()
 #>                                                                                          BFC1 
-#> "/github/home/.cache/R/BiocFileCache/5d83a5cf894_JASPAR2024_CORE_non-redundant_pfms_meme.txt" 
+#> "/github/home/.cache/R/BiocFileCache/62a79c3a692_JASPAR2024_CORE_non-redundant_pfms_meme.txt"
    diff --git a/reference/messager.html b/reference/messager.html index b462626..219fdc4 100644 --- a/reference/messager.html +++ b/reference/messager.html @@ -55,7 +55,7 @@

    Print messages

    Usage

    - 
    messager(..., v = Sys.getenv("VERBOSE") != "FALSE", parallel = TRUE)
    + 
    messager(..., v = Sys.getenv("VERBOSE") != "FALSE")
    @@ -65,11 +65,6 @@

    Argumentsv

    Whether to print messages or not.

    - -
    parallel
    -

    Whether to enable message print when wrapped -in parallelised functions.

    -

    Value

    diff --git a/reference/plot_enrichment_individual.html b/reference/plot_enrichment_individual.html index 91aacd3..a35deac 100644 --- a/reference/plot_enrichment_individual.html +++ b/reference/plot_enrichment_individual.html @@ -170,7 +170,7 @@

    Examples print(plt) } #> <div class="plotly html-widget html-fill-item" id="htmlwidget-8a1f8f4a61c98a07d1d5" style="width:100%;height:400px;"></div> -#> <script type="application/json" data-for="htmlwidget-8a1f8f4a61c98a07d1d5">{"x":{"data":[{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[66,50,48,49,15,3],"x":[1,2,3,4,5,6],"y":[34,70,79,78,67,54],"text":["<b>Peak Count:<\/b> 34 (68.42%)","<b>Peak Count:<\/b> 70 (72.53%)","<b>Peak Count:<\/b> 79 (62.2%)","<b>Peak Count:<\/b> 78 (61.42%)","<b>Peak Count:<\/b> 67 (81.71%)","<b>Peak Count:<\/b> 54 (94.74%)"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(255,0,0,1)","line":{"width":1.8897637795275593,"color":"transparent"}},"name":"No","legendgroup":"No","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[0,0,0,0,0,0],"x":[1,2,3,4,5,6],"y":[66,50,48,49,15,3],"text":["<b>Peak Count:<\/b> 66 (31.58%)","<b>Peak Count:<\/b> 50 (27.47%)","<b>Peak Count:<\/b> 48 (37.8%)","<b>Peak Count:<\/b> 49 (38.58%)","<b>Peak Count:<\/b> 15 (18.29%)","<b>Peak Count:<\/b> 3 (5.26%)"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(0,255,255,1)","line":{"width":1.8897637795275593,"color":"transparent"}},"name":"Yes","legendgroup":"Yes","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null}],"layout":{"margin":{"t":23.305936073059364,"r":7.3059360730593621,"b":59.898613393879913,"l":43.105022831050235},"plot_bgcolor":"rgba(235,235,235,1)","paper_bgcolor":"rgba(255,255,255,1)","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724},"xaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[0.40000000000000002,6.5999999999999996],"tickmode":"array","ticktext":["All<br /> CTCF_ChIP <br />Peaks","All<br /> CTCF_TIP <br />Peaks","Common<br /> CTCF_ChIP <br />Peaks","Common<br /> CTCF_TIP <br />Peaks","Unique<br /> CTCF_ChIP <br />Peaks","Unique<br /> CTCF_TIP <br />Peaks"],"tickvals":[1,2,3,3.9999999999999996,5,6],"categoryorder":"array","categoryarray":["All<br /> CTCF_ChIP <br />Peaks","All<br /> CTCF_TIP <br />Peaks","Common<br /> CTCF_ChIP <br />Peaks","Common<br /> CTCF_TIP <br />Peaks","Unique<br /> CTCF_ChIP <br />Peaks","Unique<br /> CTCF_TIP <br />Peaks"],"nticks":null,"ticks":"outside","tickcolor":"rgba(51,51,51,1)","ticklen":3.6529680365296811,"tickwidth":0.66417600664176002,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.68949771689498},"tickangle":-45,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(255,255,255,1)","gridwidth":0.66417600664176002,"zeroline":false,"anchor":"y","title":{"text":"Peak Groups","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"hoverformat":".2f"},"yaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[-6.3500000000000005,133.34999999999999],"tickmode":"array","ticktext":["0","50","100"],"tickvals":[0,50,99.999999999999986],"categoryorder":"array","categoryarray":["0","50","100"],"nticks":null,"ticks":"outside","tickcolor":"rgba(51,51,51,1)","ticklen":3.6529680365296811,"tickwidth":0.66417600664176002,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.68949771689498},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(255,255,255,1)","gridwidth":0.66417600664176002,"zeroline":false,"anchor":"x","title":{"text":"Peak Count","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"hoverformat":".2f"},"shapes":[{"type":"rect","fillcolor":null,"line":{"color":null,"width":0,"linetype":[]},"yref":"paper","xref":"paper","x0":0,"x1":1,"y0":0,"y1":1}],"showlegend":true,"legend":{"bgcolor":"rgba(255,255,255,1)","bordercolor":"transparent","borderwidth":1.8897637795275593,"font":{"color":"rgba(0,0,0,1)","family":"","size":11.68949771689498},"title":{"text":"Motif Present","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"traceorder":"reversed"},"hovermode":"closest","barmode":"relative"},"config":{"doubleClick":"reset","modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false},"source":"A","attrs":{"3a17532157cd":{"x":{},"y":{},"fill":{},"text":{},"type":"bar"}},"cur_data":"3a17532157cd","visdat":{"3a17532157cd":["function (y) ","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script> +#> <script type="application/json" data-for="htmlwidget-8a1f8f4a61c98a07d1d5">{"x":{"data":[{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[66,50,48,49,15,3],"x":[1,2,3,4,5,6],"y":[34,70,79,78,67,54],"text":["<b>Peak Count:<\/b> 34 (68.42%)","<b>Peak Count:<\/b> 70 (72.53%)","<b>Peak Count:<\/b> 79 (62.2%)","<b>Peak Count:<\/b> 78 (61.42%)","<b>Peak Count:<\/b> 67 (81.71%)","<b>Peak Count:<\/b> 54 (94.74%)"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(255,0,0,1)","line":{"width":1.8897637795275593,"color":"transparent"}},"name":"No","legendgroup":"No","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[0,0,0,0,0,0],"x":[1,2,3,4,5,6],"y":[66,50,48,49,15,3],"text":["<b>Peak Count:<\/b> 66 (31.58%)","<b>Peak Count:<\/b> 50 (27.47%)","<b>Peak Count:<\/b> 48 (37.8%)","<b>Peak Count:<\/b> 49 (38.58%)","<b>Peak Count:<\/b> 15 (18.29%)","<b>Peak Count:<\/b> 3 (5.26%)"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(0,255,255,1)","line":{"width":1.8897637795275593,"color":"transparent"}},"name":"Yes","legendgroup":"Yes","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null}],"layout":{"margin":{"t":23.305936073059364,"r":7.3059360730593621,"b":59.898613393879913,"l":43.105022831050235},"plot_bgcolor":"rgba(235,235,235,1)","paper_bgcolor":"rgba(255,255,255,1)","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724},"xaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[0.40000000000000002,6.5999999999999996],"tickmode":"array","ticktext":["All<br /> CTCF_ChIP <br />Peaks","All<br /> CTCF_TIP <br />Peaks","Common<br /> CTCF_ChIP <br />Peaks","Common<br /> CTCF_TIP <br />Peaks","Unique<br /> CTCF_ChIP <br />Peaks","Unique<br /> CTCF_TIP <br />Peaks"],"tickvals":[1,2,3,3.9999999999999996,5,6],"categoryorder":"array","categoryarray":["All<br /> CTCF_ChIP <br />Peaks","All<br /> CTCF_TIP <br />Peaks","Common<br /> CTCF_ChIP <br />Peaks","Common<br /> CTCF_TIP <br />Peaks","Unique<br /> CTCF_ChIP <br />Peaks","Unique<br /> CTCF_TIP <br />Peaks"],"nticks":null,"ticks":"outside","tickcolor":"rgba(51,51,51,1)","ticklen":3.6529680365296811,"tickwidth":0.66417600664176002,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.68949771689498},"tickangle":-45,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(255,255,255,1)","gridwidth":0.66417600664176002,"zeroline":false,"anchor":"y","title":{"text":"Peak Groups","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"hoverformat":".2f"},"yaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[-6.3500000000000005,133.34999999999999],"tickmode":"array","ticktext":["0","50","100"],"tickvals":[0,50,99.999999999999986],"categoryorder":"array","categoryarray":["0","50","100"],"nticks":null,"ticks":"outside","tickcolor":"rgba(51,51,51,1)","ticklen":3.6529680365296811,"tickwidth":0.66417600664176002,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.68949771689498},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(255,255,255,1)","gridwidth":0.66417600664176002,"zeroline":false,"anchor":"x","title":{"text":"Peak Count","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"hoverformat":".2f"},"shapes":[{"type":"rect","fillcolor":null,"line":{"color":null,"width":0,"linetype":[]},"yref":"paper","xref":"paper","x0":0,"x1":1,"y0":0,"y1":1}],"showlegend":true,"legend":{"bgcolor":"rgba(255,255,255,1)","bordercolor":"transparent","borderwidth":1.8897637795275593,"font":{"color":"rgba(0,0,0,1)","family":"","size":11.68949771689498},"title":{"text":"Motif Present","font":{"color":"rgba(0,0,0,1)","family":"","size":14.611872146118724}},"traceorder":"reversed"},"hovermode":"closest","barmode":"relative"},"config":{"doubleClick":"reset","modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false},"source":"A","attrs":{"39ad428af7a8":{"x":{},"y":{},"fill":{},"text":{},"type":"bar"}},"cur_data":"39ad428af7a8","visdat":{"39ad428af7a8":["function (y) ","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script> # }

    diff --git a/reference/save_peak_file.html b/reference/save_peak_file.html index 745ae85..bb1cb63 100644 --- a/reference/save_peak_file.html +++ b/reference/save_peak_file.html @@ -100,7 +100,7 @@

    Examples out <- save_peak_file(CTCF_ChIP_peaks, save = TRUE, "test_peak_file.bed") print(out) -#> [1] "/tmp/RtmpZzzMHV/test_peak_file.bed" +#> [1] "/tmp/RtmpvWobol/test_peak_file.bed" diff --git a/reference/to_plotly.html b/reference/to_plotly.html index ed26956..02aa9ea 100644 --- a/reference/to_plotly.html +++ b/reference/to_plotly.html @@ -109,7 +109,7 @@

    Examplesp <- ggplot2::ggplot(x, ggplot2::aes(x = a, y = b)) + ggplot2::geom_point() MotifPeeker:::to_plotly(p, html_tags = FALSE)
    - +