mathelab/altre

ALTered Regulatory Elements

altre's Issues

ShinyApp Issues

Download buttons do not work.
Step6 forward do not work.

loadCSV output error

Implement a better error message when the input CSV file doesn't have all the correct column names...

runGreat function error

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

1. A549SpecificByIntensity
2. Ambiguous
3. SAECSpecificByIntensity
4. Shared

plot titles

The titles get squished. We probably need to reposition the title, make it shorter, or add empty space.

Write functions no longer work

The download buttons in Steps 3, 6, 8 are no longer functional.

plotting function errors

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]

Error Reading in Peaks

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!

labels for step 6

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

Issue with plotting method comparison

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

graph labels in shiny

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.

Defined but not used warnings

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

legend for plotGREATenrich

The plotGREATenrich now works but the color scheme/range should be changed? Also the range should always be between 0 and 1.

progress bar

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....

3.3.2 testing

Test package on 3.3.2 and ensure it works.

Error in downloading sample csv data

hi i can not download the sample csv data from this site : https://raw.githubusercontent.com/mathelab/AltreDataRepo/master/DNaseEncodeWindows.csv

Error in plotGetCounts()

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!

Table in Step 7

The table corresponding to the pie charts is not showing

Step 7 no longer works

error: length of 'dimnames' [1] not equal to array extent

Modify CSV

Remove filepath and retrieve filepath automatically...

highcharts

Convert all plots to highcharts using branch "webgraphs"

Rounding

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) +' %'; } }

nonfatal error

Warning: Error in if: argument is of length zero
Stack trace (innermost first):
    71: RColorBrewer::brewer.pal
    70: plotGetCounts [~/ALTRE/R/plottingfunctions.R#316]

vignette suppress messages

The vignette is still outputting unnecessary lines. Need to suppress all messaging...

Volcano plot

The Volcano plot takes a very long time to render

Heatmap colors

Color gradation needs to be flipped so lower p-values are darker.

missing download buttons

Download buttons in steps 7 (writeCompareRE()) and 8 (writeGREATpath()) are missing.

Assigning Target genes

Check out GREAT and ChIP-Enrich to give options other than nearest gene...

error at annotate peak step

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!

error reading peak files

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?

Fix colors in pie chart

they should be the same color-scheme as plots in step 6 (volcano/boxplots)

Error in combine and annotate peaks step

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

pathway enrichment heatmap

The legend needs a title, and p-values in legend should be in scientific notation, rounded at 2 digits.

ALTRE not installing on windows

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

Reshape2

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

color palette

CompareMethods plot: the color palette doesn't seem to work.

Venn Diagram to Pie Charts

We no longer have Venn diagrams. We should change Venn diagrams to pie charts in the documentation.

Example code names don't correspond with the vignette

variable names in the documentation are different from those in the vignette

Adding gene names

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>

margins

The code and text go over the standard 80 characters per line standard. In RStudio, you can change the global options to display the margin.

commented and unneeded code

Do we still need ggplot2? Also, there are places were there is commented code that is probably is no longer needed.

color palettes

Can those be placed underneath or on top of the plot?

pathway enrichment heatmap

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...