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View Code? Open in Web Editor NEWALTered Regulatory Elements
Home Page: http://mathelab.github.io/ALTRE/
ALTered Regulatory Elements
Home Page: http://mathelab.github.io/ALTRE/
Download buttons do not work.
Step6 forward do not work.
Implement a better error message when the input CSV file doesn't have all the correct column names...
This for loop will fail
for (i in c("Experiment Specific", "Reference Specific", "Shared")) {
print(paste("Running", i))
mypeaks <- as.data.frame(peaks$analysisresults)[
which(table(peaks$analysisresults$REaltrecateg) == i),
c("chr", "start", "stop")]
since
peaks$analysisresults$REaltrecateg
contains four categories
The download buttons in Steps 3, 6, 8 are no longer functional.
There are argument is of length zero errors at these lines:
plottingfunctions.R #177
plottingfunctions.R #397
plottingfunctions.R#536
Warning: Error in if: argument is of length zero
Stack trace (innermost first):
81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177]
80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302]
79: func
78: origRenderFunc
77: output$annotatebarplot
2: shiny::runApp
1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Warning: Error in if: argument is of length zero
Stack trace (innermost first):
80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397]
79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312]
78: origRenderFunc
77: output$densityplot
2: shiny::runApp
1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]
Warning: Error in if: argument is of length zero
Stack trace (innermost first):
81: plotCountAnalysis [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#536]
Hello,
I was trying to use ALTRE to perform some differential accessibility analysis on my mouse ATAC-seq data and ran into problems while following the vignette. Although I have loaded and read in my peak/bed files successfully, I'm faced with an error message stating that: "Peaks must be a GRangesList Object" even though running samplePeaks shows that the peaks are GRangesList Objects. Any help you could provide would be much appreciated!
Updating the volcano plot takes a minute. If we add user inputed titles, it would be a good idea to move the data preprocessing outside the plotting function
I just wanted to inform you about an issue with the plotCompareMethodsAll() function. I wondered about the figures I got with the function, as it looked as if the intensity pie charts and peak pie charts were reversed. Therefore, I checked the code for the function here on Github and found that when the matrix is created for the plot "Intensity" and "Peak" are reversed. So indeed the Intensity pie charts actually show the Peak data and the Peak pie charts show the Intensity data.
Best, Jenny
Incorporate capability of changing label names in shiny for all functions.
Currently, steps 2 and 3 are done and functional.
Step 4 (density plot) does not work in shiny - for some reasons labels are not appearing in the shiny plot, but are in the console.
Remaining steps need to be implemented.
These lines are either not needed or contain unused variables
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L747
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L810
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L816
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L1025
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L1026
The plotGREATenrich now works but the color scheme/range should be changed? Also the range should always be between 0 and 1.
The progress bar for step 5 reads "Annotating Peaks", should read "Counting reads"
For step 6: if I run a 2nd time after changing parameters, progress bar does not appear.
For step 9a: progress bar reads "Comparing Methods", should read "Running GREAT"
There might be more....
Test package on 3.3.2 and ensure it works.
hi i can not download the sample csv data from this site : https://raw.githubusercontent.com/mathelab/AltreDataRepo/master/DNaseEncodeWindows.csv
Hi,
trying ALTRE package i have just realysed that there is a problem in plotGetCounts function:
Error in function_list[i] : could not find function "hc_add_series_density"
I was looking for a solution and I saw that highcharter package was uploaded the 17th of January (version 0.5.0) with some changes in the functions, in this case, the new one is hc_add_series.density.
I solved the problem by installing the previous version of highcharter (0.4.0), so in fact I am just wirting this to notice you about that, maybe you want to comment it in README or something.
Thank you for creating the ALTRE package, seems to be very useful!
The table corresponding to the pie charts is not showing
error: length of 'dimnames' [1] not equal to array extent
Remove filepath and retrieve filepath automatically...
Convert all plots to highcharts using branch "webgraphs"
I am not sure if rounding is necessary here . We just need to have Highcharts format the output. A quick web search gave me this
tooltip: { formatter: function() { return '<b>'+ this.point.name +'</b>: '+ Math.round(this.percentage) +' %'; } }
Warning: Error in if: argument is of length zero
Stack trace (innermost first):
71: RColorBrewer::brewer.pal
70: plotGetCounts [~/ALTRE/R/plottingfunctions.R#316]
The vignette is still outputting unnecessary lines. Need to suppress all messaging...
The Volcano plot takes a very long time to render
Download buttons in steps 7 (writeCompareRE()) and 8 (writeGREATpath()) are missing.
Check out GREAT and ChIP-Enrich to give options other than nearest gene...
I'm trying to do the tutorial workflow and I get this message at the annotate peak step:
Warning: 'ensembldb::SeqnameFilter' is deprecated.
Use 'SeqNameFilter' instead.
See help("Deprecated")
Warning: 'ensembldb::GeneidFilter' is deprecated.
Use 'GeneIdFilter' instead.
See help("Deprecated")
Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'
Stack trace (innermost first):
126: validObject
125: initialize
124: initialize
123: new
122: ensembldb::GeneidFilter
121: is
120: .processFilterParam
119: .local
118: transcripts
117: transcripts
116: ensembldb::promoters
115: ensembldb::promoters
114: getTSS
113: eval [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#57]
112: eval
111: withProgress
110: eventReactiveHandler [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#52]
90: combineAnnotateObj
89: eval
88: eval
87: inherits
86: isTruthy
85: fun_
84: dotloop
83: req
82: renderDataTable [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#280]
81: func
80: origRenderFunc
79: output$table3
2: shiny::runApp
1: runShinyApp
Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'
Stack trace (innermost first):
93:
92: stop
91: combineAnnotateObj
90: eval
89: eval
88: inherits
87: isTruthy
86: fun_
85: dotloop
84: req
83: plotCombineAnnotatePeaks
82: renderUI [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#315]
81: func
80: origRenderFunc
79: output$annotatebarplot
2: shiny::runApp
1: runShinyApp
Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'
Stack trace (innermost first):
86:
85: stop
84: combineAnnotateObj
83: vbox_fun [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#420]
82: shiny::renderUI
81: func
80: origRenderFunc
79: output$statusbox3
2: shiny::runApp
1: runShinyApp
since I'm new to this and would LOVE to use it on my own data any help would be great!
Using loadBedFiles() function to read peak files I am facing error
"Error in loadBedFiles("csv_data") : csvfile must be a data.frame "
Can anyone tell me what could be the error?
they should be the same color-scheme as plots in step 6 (volcano/boxplots)
Hi,
I keep getting the following error message when I try to combine and annotate my data:
Warning: Error in [[<-: 180817 elements in value to replace 181590 elements
Am I doing something wrong or is this a bug?
Cheers
The legend needs a title, and p-values in legend should be in scientific notation, rounded at 2 digits.
Error message from appveyor: Skipping download of Rtools because src/ directory is missing.
Package required but not available: 'Rsubread'
Rsubread was added as a package to increase performance of package (MUCH faster, eliminates hang-ups), but Rsubread is not available on windows.
Possible solutions that incorporate Rsubread:
MinGW
The reshape2 package is not needed if we are using tidyr. This line needs to be changed
https://github.com/Mathelab/ALTRE/blob/webgraphs/R/plottingfunctions.R#L291
CompareMethods plot: the color palette doesn't seem to work.
We no longer have Venn diagrams. We should change Venn diagrams to pie charts in the documentation.
variable names in the documentation are different from those in the vignette
To add the gene names, I modified your function from
tssannotgrange <- function(grange, TSS, distancefromTSS) {
# read in TSS, make column header, change to
# Granges Find distance to transcription
# start site
distancetoTSS <- distanceToNearest(grange, TSS)
# make dataframe from grange
newdataframe <- grangestodataframe(grange)
newdataframe$distance <- mcols(distancetoTSS)$distance
newdataframe <- within(newdataframe, {
region <- ifelse(distance <= distancefromTSS,
"TSS-proximal",
"TSS-distal")
})
# annotate anything <=1500 bp away as
# TSS-proximal, otherwise TSS-distal
chr <- c()
annotatedgrange <- with(newdataframe,
GRanges(chr,
IRanges(start, stop),
meta = newdataframe[, 5]))
# create a grange
colnames(mcols(annotatedgrange)) <- c("region")
return(annotatedgrange)
}
to
tssannotgrange <- function(grange, TSS, distancefromTSS) {
distancetoTSS <- distanceToNearest(grange, TSS)
mcols(grange)$region <- ifelse(mcols(distancetoTSS)$distance <= distancefromTSS,
"TSS-proximal",
"TSS-distal")
mcols(grange)$gene_name <- mcols(TSS[subjectHits(distancetoTSS), ])$gene_name
return(grange)
}
so the output is exactly the same but with an additional column (i.e. gene_name)
GRanges object with 256132 ranges and 2 metadata columns:
seqnames ranges strand | region gene_name
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr1 [ 10146, 10349] * | TSS-distal DDX11L1
[2] chr1 [237719, 237910] * | TSS-proximal AP006222.2
[3] chr1 [521551, 521614] * | TSS-proximal RP5-857K21.2
[4] chr1 [564454, 565042] * | TSS-proximal MTND2P28
[5] chr1 [565253, 566084] * | TSS-proximal MTND2P28
... ... ... ... . ... ...
[256128] chrY [59019677, 59020088] * | TSS-distal CTBP2P1
[256129] chrY [59020581, 59020934] * | TSS-distal CTBP2P1
[256130] chrY [59024187, 59024559] * | TSS-distal CTBP2P1
[256131] chrY [59027624, 59027997] * | TSS-distal CTBP2P1
[256132] chrY [59029576, 59030134] * | TSS-distal CTBP2P1
The problem now is that the rest of the code needs to be modified since downstream functions assume that region is the last column. As a result, you get something like this
$consPeaksAnnotated
GRanges object with 195887 ranges and 4 metadata columns:
seqnames ranges strand | meta.region meta.A549 meta.SAEC meta.NA
<Rle> <IRanges> <Rle> | <character> <character> <character> <character>
[1] chr1 [ 10146, 10349] * | TSS-proximal DDX11L1 A549 <NA>
[2] chr1 [237719, 237910] * | TSS-proximal AP006222.2 A549 <NA>
[3] chr1 [521551, 521614] * | TSS-proximal RP5-857K21.2 <NA> <NA>
[4] chr1 [564454, 570272] * | TSS-proximal RP5-857K21.11 A549 <NA>
[5] chr1 [713897, 715323] * | TSS-proximal RP11-206L10.9 A549 <NA>
... ... ... ... . ... ... ... ...
[195883] chrY [59003875, 59006774] * | TSS-distal CTBP2P1 A549 <NA>
[195884] chrY [59011978, 59020934] * | TSS-distal CTBP2P1 A549 <NA>
[195885] chrY [59024187, 59024559] * | TSS-distal CTBP2P1 A549 <NA>
[195886] chrY [59027624, 59027997] * | TSS-distal CTBP2P1 A549 <NA>
[195887] chrY [59029576, 59030134] * | TSS-distal CTBP2P1 <NA> <NA>
Do we still need ggplot2? Also, there are places were there is commented code that is probably is no longer needed.
Can those be placed underneath or on top of the plot?
to ensure readability of results, the heatmap showing pathway enrichment should be capped to 10 pathways per each RE type. Users can then download results from Excel file and modify if needed.
Or we could include a parameter so users chose how many pathways they want to input...
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