NEWS.md
In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

splicejam 0.0.82.900

Moved functions into separate files for better code review.
getGRcoverageFromBw()
When it fails to download a bigwig file, it prints the error which is not always informative. Now it also prints the warning, which can tell whether the URL was available, or another error was caused by this step.

splicejam 0.0.81.900

Removed shinyWidgets::setShadow() to prevent the warning message saying this function is being deprecated.
Fixed bug "width() not found" caused by missing package prefix.

Help docs for launchSashimiApp() now include Troubleshooting
It includes two potential workarounds for errors caused by failure to download the coverage file from a remote server.

splicejam 0.0.80.900

Updates to address Shiny app error: "object 'covNameL' not found"
This bug occurs when there is no coverage, and seems to occur when the connection to the server coverage files is not available.
combineGRcoverage() was updated to sidestep the covNameL error, although it may not fully resolve the underlying problem of missing coverage data. Tests are ongoing, since the underlying problem is difficult to reproduce. Theories:
- Server file cache reached its maximum and no longer permits new cache files from being stored.
- Previously saved cache file may be corrupted, although errors are intended to cause the cache to be invalidated, therefore refreshing the data from the server.
- Disconnection from the server that provides coverage and junction data.
Miscellaneous minor updates to ensure data.frame subsets all include drop=FALSE where relevant. Minor, but may help with odd cases where server data is not as expected.
grl2df()
Finally fixed the junction stacking for negative strands, see Nectin3 using default farrisdata.

splicejam 0.0.79.900

The method of labeling exons was updated to enforce placement below exons, and to expand the ggplot2 whitespace below the exons using ggplot2::expansion() which uses a multiple of plot height.

With ggplot2 version 3.5 and higher, trans objects are deprecated in favor of transform objects. The conversion as.transform() is buggy, it fails when provided a trans object to convert to transformation - which can happen when using R-shiny cached data with launchSashimiApp(), which stores objects in subfolder sashimi_memoise/. These objects may have stored trans objects, which s
Many functions were modified not to use require(package)
Major changes to underlying R code which could cause errors for any un-prefixed package function call.
Numerous changes to add package prefixing, packages including jamba, GenomicRanges, IRanges, S4Vectors, shiny, others. I was really lax originally, using require() to avoid proper prefixing.
Full tests were completed, mainly running the live R-shiny app launchSashimiApp() which touches nearly every aspect of this package.

make_ref2compressed() returns the output from scales::trans_new() which changed output from trans to transform in newer versions of scales, consistent with ggplot2 version 3.5 and higher, see previous point.
The output of make_ref2compressed() with newer versions of scales and ggplot2 includes a transform object.
Fortunately, all splicejam functions can make equivalent use of trans or transform objects, provided they were created with the same R package versions for scales and ggplot2.
When in doubt, if observing errors "covNamesL not found" or similar, try deleting memoise cache subfolders, update R packages, then try again.
gene2gg() - The method for rendering exon labels was updated:
It uses expand=ggplot2::expansion() to extend the y-axis by a multiple of the plot height, making it more reliable to add enough whitespace to fit exon labels.
Exon labels are pushed slightly lower than before (-0.2 instead of -0.1), and use ylim to constrain all labels below the exon. Previously with many exon labels, they would be pushed up or down, making a tangled mess.
Exons labels use min.segment.length=0 and always draws a line segment.
In principle, even for genes like Zbtb20, the exon labels should be much more visible, positioned below the exon plot, and will use two rows to minimize overlapping labels.

splicejam 0.0.78.900

plotSashimi()
New optional argument junc_nudge_pct to control the nudge_y placement of junction labels relative to the top edge of the junction ribbon.
Previously, labels may randomly be placed below or above the top edge of the ribbon.
The new default junc_nudge_pct=0.05 slightly moves labels up by 5% the max y-axis junction label position, which makes all labels appear consistently above the ribbon.
Negative values will place the label below the top edge of the ribbon.
A vector with multiple values can be supplied, in order to control the position of each individual label.
gene2gg()
Added nudge_y=-0.2 by default (not configurable) to help position exon labels below the gene structure.
New default hjust=0.5 changed from hjust=-0.2 which caused labels to be slightly shifted left. (I do not think the previous effect was actually intended.)

splicejam 0.0.77.900

readGtf() is a small helper function to load GTF/GFF3 files, called by makeTx2geneFromGtf() and describeGtfAttrNames().
describeGtfAttrNames() is a simple helper function to print a quick data.frame for each source (column 2) in a GTF/GFF3 file, the attribute names and values observed in column 9.

makeTx2geneFromGtf()
Updated to handle gff3 format in addition to gtf format.
new argument zcat_command used to specify the call to zcat or gzcat, only used when input is gzipped and R.utils is not installed.
Fixed issue when transcript attribute names are not consistently represented on all rows in gtf/gff3 output. Formerly the output fields would contain the full semicolon-delimited values from column 9, instead of replacing unaltered entries with '' empty string.
bgaPlotly3d()
A more complete refactor of this function is in progress, to simplify the code, to allow exporting individual data.frame objects for the visual components displayed in plotly.
The original function used rgl, and was ported to plotly to help render on Rmarkdown documents in HTML form. However, the rgl package can also create HTML export, and makes slightly nicer figures, at the expense of not having customized mouseover text labels. (Even though labels are incredible difficult to customize in plotly.) The rgl package has additional 3D shapes that could help when rendering the cross-group block arrows, and could be useful to apply shape to experiment design factors.
A plotly error occurred when drawSegments="genes" due to mismatch in expected values in column "textposition" during plotly rendering. This error may have occurred during a recent plotly update, the workaround is simply not to include "textposition" during display of gene vectors, which causes them to default to use textposition="top center".
geneColor can now be a named vector, to allow colorizing individual genes by name.

splicejam 0.0.76.900

Issue #3 reported jamGeomean() was not honoring na.rm=TRUE, this issue has been resolved. Also geomean() was updated to ensure that na.rm=TRUE also results in returning a non-NA value, except in cases where all input values are NA in which case it returns NaN consistent with mean.default().

splicejam 0.0.75.900

Bug was reported on edge cases with positive strand CB samples. It appears to be an edge case derived from rare duplicated names() in splice junction GRanges, fortuitous for certain genes. The duplicate names are repaired in prepareSashimi() hopefully resolving downstream effects. The duplicate names appear to originate from import_juncs_from_bed(), unclear why the issue was not seen before now, could be subtle change that added rownames that previously did not exist somewhere upstream in the process.
Aside: The bug is intriguing partly by the way is was observed: only when all CB samples were shown, and only on the positive strand. I think the cause is related to an upstream step adding numeric names to splice junctions in order they appear, and they happen to be loaded one sample_id at a time. When selective a particular gene, it combines junctions from each requested sample_id, after subsetting each for the requested gene. In principle it would be rare that the same range of entries is used from multiple samples - for example entries 9500 through 9575 from CA1_CB and entries 9570 through 9800 from DG_CB. But it tends to happen across CB samples and not between CB and DE samples, which suggests the CB samples are more similar to each other than they are to DE samples.

splicejam 0.0.74.900

Added package R.utils to Imports, since it is required by data.table to import gzip files.

Added @import data.table to import_juncs_from_bed() and other functions, sometimes it is required for full functionality from data.table.

splicejam 0.0.73.900

import_juncs_from_bed() was updated to force printing the actual R error message, in addition to internal error reporting where the error occurred. We suspect data.table::fread() or openssl may not be reading the remote gzipped junction file over the https connection. It appears to be a machine-specific error not seen on multiple test machines until now.

splicejam 0.0.72.900

sashimiDataConstants() now propagates "verbose" into the data environment so the verbose flag will be persistent through the Shiny app functions.
getGRcoverageFromBw() prints more error information when retrieving coverage fails. Errors seem to happen when openssl is not enabled for "https" URLs as opposed to "http" URLs. Unclear exactly why.
import_juncs_from_bed() was updated to force printing error messages when retrieving data from cache fails, or when retrieving the junction data itself fails.

Two new config options adjust the junction arc height. We noticed for some genes, the junctions overlap the intermediate coverage, so these options allow raising the arcs accordingly.
"Junction arc factor" adjusts the relative height of junction arcs.
"Junction arc minimum" defines the minimum junction arc height.
Changed "Junction transparency" to "Junction non-transparency".
Moved "Interactive Plot" option to the top.

splicejam 0.0.71.900

import_juncs_from_bed() was updated to correct an issue where verbose output was required for the cache repair step.
sashimiAppServer() was updated to remove all %>% pipes. Ah well, adding a package prefix was not the answer to that particular issue.

splicejam 0.0.70.900

sashimiAppServer() was updated to reorganize the overall series of Shiny reactive events, cleaning up some dependencies.
sashimiAppUI() new query device to control the gene-transcript-exon panel height independent of the sashimi coverage plot panels.

Wrapping Shiny functions in an environment was a clever way to pass variables directly from an active R session. It also means the data can remain inside the environment without copying it into each function - while also allowing data to be updated and saved in that environment.

However it appears to break the R package import process, and caused %>% to be unknown even though the dplyr package was supposed to imported. I cannot understand the import scope - it works sometimes but not other times. Maybe because the environment does not have a parent, it causes imported functions to be lost?

sashimiAppServer() was updated to fix missing %>%, and other issues that arose with the new data environment workflow.
sashimiAppServer() briefly broke the ggplotly workflow for interactive plots, because plotly::subplot() absolutely choked and failed when the numeric vector heights had names. So that was fun... removing names from heights fixed the error.
Another bug appears to be causing splice junctions to be invisible on the public site, despite being present in all internal test instances.

splicejam 0.0.69.900

sashimiDataConstants() is a subset of sashimiAppConstants() that includes only the required data, and not the R-shiny app components such as the help text and widgets. It was updated to store all data inside an environment, which updates data in that environment during processing as needed.
get_fn_envir() is a helper function that returns a variable value from the calling function, or from one or more provided environments. The use case is to allow a user to define function variable values directly, then to use the environment values otherwise.

launchSashimiApp() was changed so that it uses a user-supplied environment to store intermediate data for the R-shiny app. By default this environment is globalenv() for backward compatibility, however it is recommended to create a new environment to insulate data from the globalenv().
sashimiAppConstants() was updated to use environment as input and the new function get_fn_envir(). Note that previous input would ultimately use values in globalenv() even when using a specific environment. The default was to use globalenv() so that behavior was not problematic. The new behavior will strictly only use either the function argument, or the value in the specific environment provided.
import_juncs_from_bed() was refactored completely, so it is able to handle BED12 input as well as "SJ.out.tab" junction output directly from STAR alignments. This refactor will cause all previous memoise cache for junction files to be invalidated, and thus downloaded again. These files are small and fast to download, but it is worth noting. The underlying method now uses data.table::fread() then it decides whether to convert from BED format with as(bed, "GRanges") or converts from "SJ.out.tab" when there are 9 columns.
Several functions had the verbose output reduced, instead when verbose > 1 the more verbose output is printed.

splicejam 0.0.68.900

getGRcoverageFromBw() was updated to fix a bug that really originated from rtracklayer::import.bw(), which returns output sorted by the bigWig file chromosome sort order, and not by the order of rtracklayer::BigWigSelection() as documented in rtracklayer::import.bw(). The workaround implemented in getGRcoverageFromBw() is to return coverage in the exact order requested. Note this issue will not affect sashimi plots since each gene is contained within one chromosome, and in this case the coverage is returned by rtracklayer in the order it is requested within a chromsome, but rtracklayer bug returns results for each chromosome together regardless the order it was requested. Also this update was performed outside the memoise call, so the cache will store data in the order received from rtracklayer::import.bw() but will re-order those results consistent with the order of input GRanges.

splicejam 0.0.67.900

sashimiAppUI() was updated to change "Sample Selection" to use dataTable output.
sashimiAppServer() was updated to handle dataTable widget for "Sample Selection" and sample ordering, removing the previous method of drag-and-drop. The reasons: first, the drag-and-drop was not mobile-friendly; second, the widget apparently broke after the recent updates. The error was reproduced by changing the sample selection, then creating a new sashimi figure - in that case no sample selections were retained and the figure failed due to no selected samples.
sashimiAppConstants() was updated to include a text box with full sessionInfo() output, inside a box that is collapsed and hidden by default. This output is on the "Guides" tab below the section "Relevant R version info".

splicejam 0.0.66.900

sashimiAppUI() was updated to correct some visual glitches in the R-shiny app, using the shinydashboard::box() instead of shinydashboardPlus::box() except where required. The shinyWidgets::sliderTextInput() appears to detect the wrong color for title text and tick marks, so the sidebar background was changed to medium grey to try to account for those oddly inconsistent choices. It currently cannot be customized.

gene2gg() new argument geneSymbolColname allows using a specific gene symbol column name, instead of the previous default "gene_name". The corresponding ggplot2::aes() was changed to ggplot2::aes_() to allow using a variable as a name.
gene2gg() argument hjust was changed to hjust=-0.5 because somehow the apparent behavior of hjust in ggrepel has changed in recent versions. The previous value hjust=2 is roughly the same as the new value hjust=-0.5 which is... unexpected.

splicejam 0.0.65.900

Several updates were implemented to correct behavior seen only with long-running R-shiny apps, such as https://splicejam.vtc.vt.edu unfortunately. These changes should help make the R-shiny app more robust for all users, but are particularly targeted at the longer-running R-shiny servers.

The shinydashboardPlus package version 2.0.0 included numerous of "breaking changes" that also required numerous updates to the R-shiny sashimi app. Functions were renamed (dashboardHeaderPlus(), boxPlus()) and introduced name conflicts with the existing shinydashboard package - and so required package prefixing to ensure the correct function is being called.

flattenExonsBy() was updated to warn on disjoint exons correctly this time.
flattenExonsBy() several updates to ensure proper handling of detectedTx in edge cases. Code was somewhat cleaned up to make each step more clear.
sashimiAppServer() was updated to force several instances of default behavior for some form components that apparently do not return values upon the initial start-up of the R-shiny app. This behavior may be fixed properly in future, so that the values are initially available. For now, the fallback to use default values is chosen.
sashimiAppServer() fixed bug where detectedTx was not showing even when check box "Show transcripts" and "Detected only" were both checked. In future unchecking "Detected only" should include more transcripts for genes that have a subset of detected transcripts, thus widening the field of view so to speak.
sashimiAppConstants() was updated to print more detail regarding detectedTx entries during the preparation steps. When there are no detectedTx entries that match tx2geneDF$transcript_id then it prints the first 20 lines of tx2geneDF for visual review. In these cases the resolution might be to remove the local file ".tx2geneDF.txt" which will force the file to be re-created from the GTF source file, and may resolve the mismatch.

Apparently for .tx2geneDF.txt files that existed in older versions of splicejam, the stored file included rownames that were ignored upon load. When splicejam switched to use data.table::fread() and data.table::fwrite() it briefly broke the ability to keep the header line because header=TRUE was not working as expected. Removing header=TRUE causes data.table to detect the rownames and add a new column which is ignored. All future versions of splicejam should not be affected.

splicejam 0.0.64.900

Added "testthat" package dependency, which requires version 3.0.0 or higher to avoid the bug associated with testthat_print() not found.
assignGRLexonNames() was updated to include examples, and to remove a redundant step when checking for disjoint ranges. The process was updated to clarify how geneSymbol values are obtained, from values(GRL)[[geneSymbolColname]], values(GRL@unlistData)[[geneSymbolColname]], then names(GRL) in order of the first one with valid values. It now also handles the case where names(GRL) is not defined, but where values are present via geneSymbolColname.
jam_isDisjoint() was updated to return a logical vector for GRangesList input, representing each GRanges element in the GRangesList. This change is consistent with GenomicRanges::isDisjoint() without sacrificing speed.

splicejam 0.0.63.900

Fixed jampack #1 bug with splicejam::gene2gg() when only flatExonsByGene is supplied without flatExonsByTx the GRangesList coersion no longer allows one object to be NULL. Workaround is to ignore the missing object which keeps everything as GRangesList without needing coersion.
Fixed bug in assignGRLexonNames() that appears to be caused by a new Bioconductor data type FactorList, which requires explicit conversion to list for this function to work as expected.
Cleaned up some errors in function examples, most just needed to have the examples re-evaluated to clear the cached error.

splicejam 0.0.62.900

makeTx2geneFromGtf() was updated to prevent edge cases in parsing GTF files, conversion to data.frame with stringsAsFactors=FALSE just to make sure, for R versions lower than 4.0.

defineDetectedTx() was updated with slight change to the percent max isoform expression. The previous calculation used the higher of max expression or 1 in the percent maximum, to prevent divide by zero. However, it assumed expression should be 1 or higher, making the resulting percentages lower than 100% max for genes whose isoforms all had values less than 1. Originally this was a feature, since genes with expression less than 1 were not beneficial, however when using TPM values it is useful to allow values less than 1. New arguments: floorTPM and floorCounts allow custom minimum values, the defaults are 0.001.

splicejam 0.0.61.900

annotateGRfromGR() was optimized for edge cases where there were a low number of multi-overlaps and large number of single-overlaps.
grl2df() was not properly stacking junctions in sashimi plots, the problem was caused by closestExonToJunctions() which annotates junctions by the nearest compatible exon boundary, with no regard to distance from the exon. The stackJunctions() function simply stacks based upon "nameFrom" and "nameTo", so junctions that land between exons were being stacked together with junctions that properly align those exons. Now closestExonToJunctions() has optional argument spliceBuffer, when supplied a distance, exons beyond that distance are annotated by exonName.distance. Novel junctions will stack only when they share the same distance from an annotated exon.

jam_isDisjoint() is a rapid alternative to GenomicRanges::isDisjoint(), that tests GRanges or GRangesList for disjoint (non-overlapping) ranges. In one test with large GRangesList, the duration was reduced from 100+ seconds to 0.5 seconds.

makeTx2geneFromGtf() was optimized again, substantially reducing the time and memory required. The rownames returned are also defined by values in colname "transcript_id" if it or similar colname exists, passed through jamba::makeNames() to ensure they are unique.
Updated help documentation for assignGRLexonNames().
Added \preformatted tags to help docs for curateVtoDF() and curateDFtoDF(), otherwise the examples are not properly formatted with whitespace.
internal_junc_score() new argument minScore=0 will return this minimum score, especially useful if for some reason the input data contains no valid score colname. Otherwise the minScore is applied to the absolute value of the score, keeping the original sign. (Zero becomes positive.)
detectedTxInfo() was updated to handle being supplied both Gene and Tx values, and a new optional argument Groups to allow returning a subset of group colnames.
defineDetectedTx() new argument applyTxPctTo defines which expression data to use (count data or TPM abundance data) for the percent max calculation. The purpose of this new argument is to specify whether to apply the percent max threshold to TPM, counts, or a combination of the two:
"TPM" uses only TPM data for percent max thresholding
"counts" uses only count data
"either" uses the higher percentage from TPM and count
"both" uses the lower percentage from TPM and count

As a result, the output is also expanded to include list elements:

"txPctMaxTxGrpAll"
"txPctMaxTxTPMGrpAll", in addition to
"txPctMaxGrpAll" still represents the data used for filtering, modified relative to applyTxPctTo.

Several changes were intended to help set up custom R-shiny apps, with specific default settings different than the Farris et al defaults.

sashimiAppConstants() was updated to enhance the logic flow, and to print more verbose and hopefully more helpful output during the process.
sashimiAppConstants() uses data.table::fread() and data.table::fwrite(). Fixed inconsistency in row.names and col.names.
sashimiAppServer() was updated to clarify some verbose output, and define default gene more robustly.
launchSashimiApp(), sashimiAppServer(), sashimiAppUI() now respect "gene" from the environment to use as the first gene loaded, instead of using "Gria1" which is intended only for the Farris et al data.
launchSashimiApp() now properly handles server-configured options such as width, server, port, and other R-shiny app options. Most important are server and port, which allows the R-shiny app to be run manually on ports above 8000 if necessary.
launchSashimiApp() now properly initializes with variables from the active R environment. More variables will be converted, along with robust error checking. For now, these variables are available:
gene which defines the first gene displayed
sample_id which defined the set of sample_id values to display
min_junction_reads - minimum junction read threshold
use_exon_names - one of c("coordinates", "exon names")
exon_range_selected - two gene_nameExon values
exon_range_choices_default - exon labels available for default gene
layout_ncol - number of columns in layout
include_strand - one of c("+","-","both") strands to display
share_y_axis - one of c(TRUE, FALSE) whether to use shared y-axis range
assignGRLexonNames() was updated to be more tolerant of "problematic GTF file" data, specifically to allow optionally keeping genes that are found on multiple strands, which previously were removed by default. The idea of keeping a multi-strand gene is not ideal when thinking about sashimi plots, but can be useful when considering gene exons, especially when genome assembly may also be unfinished. Tools such as featureCounts will generate counts across all exons for a gene, regardless of strand and chromosome, so the output from assignGRLexonNames() will be compatible. The argument filterTwoStrand=FALSE will keep features present on multiple strands (or chromosomes.)
assignGRLexonNames() now calls new function jam_isDisjoint() to test for disjoin features. For a large test GRangesList object, the duration was reduced from 60 seconds to 0.5 second.
flattenExonsBy() was also updated with new argument filterTwoStrand which is passed to assignGRLexonNames() after exons have been flattened. Use filterTwoStrand=FALSE to keep all gene features even when they are present on multiple strands or chromosomes.
flattenExonsBy() new argument exon_method which has two options:
exon_method="disjoin" is the default, which combines transcript exons per gene and maintains distinct boundaries, in case an exon is longer in one isoform than another, it is subdivided into something like c("GENE_exon1a", "GENE_exon1b").
exon_method="reduce" is a new alternative, it uses GenomicRanges::reduce() to combine exons across transcripts, and therefore ignores any subdivision of exons. In the same example above it would produce only "GENE_exon1". The main benefit from this option is that it is markedly faster for genome-wide data preparation, where "disjoin" may take 2 to 5 minutes, "reduce" may only take several seconds.

Setting up a new sashimi plot is not crystal clear, and most preparatory steps can be done once and never again (for each version of Gencode.) Ideally, install an R package that contains:

exonsByTx
cdsByTx
flatExonsByGene (all genes?)
flatExonsByTx (all transcripts?)
tx2geneDF (with fix for mis-matched transcript_id between GTF and FASTA from Gencode)
txdb (optional, but not provided by Bioconductor currently)

splicejam 0.0.60.900

groups2contrasts() updated a bug that was not maintaining factor order in two-way contrasts. Slightly enhanced logic used in argument removePairs so that it works with single factor contrasts (where that factor does not change.)
defineDetectedTx() now uses decimal values for the mean count and mean abundance group values, rounded to the 0.1 decimal place.

splicejam 0.0.59.900

defineDetectedTx() default argument value cutoffTxTPMExpr=0.1 which was previously cutoffTxTPMExpr=2. It appears that this threshold is somewhat dependent upon the input data, and that 2 was too stringent for the majority of datasets testes since the Farris et al publication. Therefore, a more suitable default value is less restrictive of low-TPM abundance values. This change also makes the count-based threshold the dominant filter for technical detection above background noise, which makes some sense because count noise is somewhat more of a hard boundary.

Overall, the changes allow some coverage data to be "missing", though it will generally try twice to retrieve coverage. When coverage is "missing" it is rendered empty, with no other error or message. This change may not be ideal, if the coverage URL is mis-typed for example, but it beneficial during a network outage.

sashimiAppServer() was updated to repeat the call to prepareSashimi() when the returned object contained a list element some_null=TRUE, which indicates that one or more underlying elements of the data was returned as NULL, indicating a failure. In this case, prepareSashimi() is called in a way that does not re-use the existing cache. Note that prepareSashimi() calls other functions, each of which caches data. If those functions return NULL, they also assign attribute attr(x, "some_null") <- NULL, which helps cascade this failure up the chain to calling functions.
import_juncs_from_bed() was updated to use tryCatch() to catch errors when the requested file cannot be retrieved. When memoise cache is being used, it will try to clear the cache then try again, or will try again without using memoise.
getGRcoverageFromBw() was updated to enhance the memoise cache repair logic: If coverage is zero-length, it tries again. Zero-length coverage can happen from a zero-length memoise cache file, or when the rtracklayer::import() function returns zero-length coverage. That tends to happen when the file is not accessible, network is down, or the path is invalid, etc. Nonetheless, memoise will happily store a zero-size cache file (!) with no clear way to remove or ignore it. So we try to call memoise::drop_cache() which only exists in memoise version 1.1.0.9000, currently on Github with no expected CRAN release timeline. If we cannot remove the cache file, we try to get coverage without using memoise. The overall summary:
If coverage is empty, try remove the empty memoise cache file.
If we removed the empty memoise cache file, we try again to retrieve coverage using memoise. The new memoise cache file will either be empty (if the source failed again), or non-empty (the second attempt was successful). If the file is non-empty, the repair worked, and future calls should use the memoise cache file without problem.
If it could not remove the empty memoise cache file, it tries to retrieve coverage again without using memoise. In this case, the empty memoise file still exists, which means all future calls will not use the cache file.
combineGRcoverage() was modified to be tolerant to missing coverage data. Typically when coverage is missing, the data returned from getGRcoverageFromBw() returns a vector of 0 values, however sometimes there is no data returned for a single URL, perhaps due to network outage. Nonetheless, combineGRcoverage() will now ignore any samples that are not present in the colnames of the GRanges object supplied.

splicejam 0.0.58.900

The launchSashimiApp() function which starts the R-shiny app sometimes encounters errors when the required files are not available, as has been the case with server or network outages. Since each requested file is stored in a memoise local file cache, a previously-accessed gene should pull from the cache and avoid these errors. But newly accessed genes result in corrupted (or zero-size) cache files. Splicejam tries to detect corrupt cache files and reload from the source (referring to filesDF) however this process is proving to be imperfect, and the sort of thing that is difficult to debug.
The remedy for weird errors in the R-shiny app is usually to remove all *_memoise subdirectories, which forces the cache to be rebuilt.
Some reference numbers regarding speed: In our testing, the typical new gene request takes about 10-20 seconds to retrieve data, assemble the ggplot object, then display the plot -- for 8 covergae files and 8 junction files. A cached gene takes about 3-5 seconds to display the plot, almost all of that time is ggplot rendering its own plot object. In principle, R-shiny has the ability to cache rendered ggplot objects, which results in response of less than 1 second for cached rendered plots. However that process only works when the cached rendered plot has identical dimensions to the newly requested plot. Splicejam currently scales the plot to size of the web browser, which means the benefit would only help each browser size. For example, splicejam works really well on a phone web browser (!), somewhat surprising to me, but it turns out to be great. I use it quite a lot when I'm on the go, between meetings, and admittedly during some meetings.

prepareSashimi() now positions junction labels at the maximum edge of the junction arc, in stranded fashion. Might consider adding text adjustment so the label is not centered at the edge.
plotSashimi() now applies scales::comma(..., accuracy=1) by default, which removed the decimal values from junction labels. Some recent update to scales::comma() seems to have caused decimal values to appear by default. A new argument junc_accuracy is passed to scales::comma(..., accuracy=junc_accuracy) to allow customization.
plotSashimi() fixed issue where junc_alpha was only being applied when data contained junctions without coverage, now the junc_alpha is applied in all cases.
sashimiAppServer() now displays the strand of the gene found in the top search pane, which allows someone to set the coverage strand consistent with the gene if desired.

splicejam 0.0.57.900

Fixed issue with plotly rendering in R-shiny context, it was throwing an error "TypeError: postRenderHandlers is undefined". Upon deeper inspection, the uiOutput() element being used to display both ggplot and ggplotly output, was somehow not providing the plotly javascript dependencies to include relevant postRenderHandlers. The workaround was to add an empty plotlyOutput("plotly_blank") to the UI, which appears to cause the required javascript dependencies to be loaded. Stackoverflow threads and Github issues suggest there exists a method to load dependencies when embedding htmlwidgets inside tagList context -- for example when embedding a custom htmlwidget inside a table cell. Perhaps the proper remedy is related.

splicejam 0.0.56.900

Fixed rare error in annotateGRfromGR() with numeric columns, which failed to initialize a new GRanges column with numeric(0) instead of using a numeric form of NA, which was accomplished with c(0, NA)[2].

splicejam 0.0.55.900

Changed plotSashimi() argument default ylab="read depth", previously it was "score". In future, normalized data might use ylab="normalized read depth" but that would be a custom option for the analyst.
plotSashimi() arguments "xlabel" and "xlabel_ref" control the x-axis label, which by default xlabel_ref=TRUE will use the reference (chromosome) as the x-axis label, which makes sense because the axis shows chromosome coordinates. The "xlabel" argument is intended to allow a fully custom label.

splicejam 0.0.54.900

Fixed bug in compressPolyM() edge case, polygons with only two x values and y values all zero; threw an error Error in x[idx1, ] : only 0's may be mixed with negative subscripts. New rule requires at least 5 x-axis values, otherwise compression doesn't seem necessary anyway.

New argument compress_introns added to exoncov2polygon() and prepareSashimi(), which determines whether to call compressPolygonM() when creating polygon coordiantes for coverage data. Setting compress_introns=FALSE saves about 20% of the time it takes to prepare sashimi data.
Changed default compressPolyM() argument from minRatio=3 to minRatio=5, the threshold of compression above which polygon coordinates are adjusted.
Changed sashimiAppServer() to create the memoise version of prepareSashimi() only once, instead of re-creating it each time. Probably no noticeable effect, but it feels better.

splicejam 0.0.53.900

New README.Rmd file with a visual example and description of a sashimi plot. New small data object "demodata" which contains the minimum required to produce the Gria1 plot.
Added splicejam hexsticker with an embedded sashimi plot. An R package isn't an R package without a hexsticker.

splicejam 0.0.52.900

Slight enhancement to prepareSashimi() to change the "name" column to a factor, in order to force the drawing order of junction arcs, so junctions are drawn in order of most dominant, to least dominant, then shorter spans to longer spans. Smaller score, wider junctions are drawn last, since they are typically the most difficult to see otherwise. "Dominant"" refers to the junction_rank calculated by having the highest score among junctions that start or end at the same coordinate: junction_rank=3 means the junction has the highest score on both sides, and has the darkest color; junction_rank=2 has the highest score on one side but not both sides, and is lighter in color; and junction_rank=1 does not have the highest score on either side of the junction, and has the lightest color. The junction_rank=1 entries are now drawn last, since they typically have the lowest scores, and are small and thus easily obscured.

splicejam-sashimi-server() was updated to handle changes in the gene search field properly, avoiding edge cases with un-detected genes that have no sashimi data.
prepareSashimi() was updated to handle absence of splice junction data, in a more robust way.
spliceGR2junctionDF() was updated to handle missing junction data, ultimately returning NULL which is easier handle consistently by other downstream functions. Also made small update to handle sample_id as a factor when input data is supplied only as a GRanges object.

splicejam 0.0.51.900

bgaPlotly3d() new argument sampleGroups allows data to be re-grouped to define custom group centroids. Main driver is when running BGA on un-grouped data, for example where each replicate is its own group. Using sampleGroups allows the proper sample group to be highlighted on the plot. This scenario is mainly only advised when needing to run standard PCA or COA, or when there are fewer than four groups, since BGA produces n-1 dimensions. Code was also slightly update to prepare for broader use outside of BGA.
bgaPlotly3d() was updated to handle the "textposition" argument to plotly labels, allowing individual adjustment of each centroid and sample label.
bgaPlotly3d() new argument geneLabels allows replacing gene identifier with a custom label, for example replacing assay ID with gene symbol.
gene2gg() updated to maintain a minimum y-axis range when labelExons=FALSE. Previously the exons could be cropped.

bgaPlotly3d() bug fixed which prevented display of scaled coordinates from the bgaInfo object, mainly because the scaled coordinates are not supplied for individual samples. Instead the scaling factor (adjustment used to convert centroid coordinates from raw to scaled) is applied to sample coordinates to produce equivalent scaled coordinates. That said, I recommend using un-scaled coordinates, which keeps the x, y, and z axis scales proportional to their relative contribution, which visually reinforces the relative strength of separation in each dimension.

splicejam 0.0.50.900

Fixed regression in stat_diagonal_wide_arc() which calls ggforce::StatBezier. Version 3.1.0 of ggforce changed the required call to that function, breaking the dependency and causing junction arcs to be invisible as a result. The new interface mimics how ggforce::stat_diagonal_wide() calls ggforce::StatBezier. I hope the interface does not change in future.
Added package version dependency for ggforce version 0.3.1, which is the point where the API changed with ggforce::StatBezier.
Fixed vignettes which assumed optional R packages were installed, for example org.Mm.eg.db. Now if the package is not available, it skips the corresponding sections.

splicejam 0.0.49.900

Updated the "Guides" tab of the R-shiny Sashimi app. It now also prints the R version, and the package versions of jam packages.
Updated DESCRIPTION to include higher specific version numbers for several packages, to force an update if needed.
Updated vignette to remove hard dependency on the tximportData package, making it optional. This change prevents the 250 MB package from being required only for the example vignette. In future, a random generated expression data matrix may be created.

splicejam 0.0.48.900

Fixed small bug in getGRcoverageFromBw() that used default memoise path "memoise_coverage" instead of "coverage_memoise" as with other functions. Only affected directly calling getGRcoverageFromBw() since other functions passed the directory as an argument, and thus probably only me.

The default plotly does not enable highlighting. It is currently too slow and laggy, subject of future optimization.
Font sizing is reworked, to start with 14 point font and add/subtract from that font size. It converts to ggplot2 convention of "mm" units, since it appears to ignore grid "pt" units. The bast plot font size can be adjusted, affecting everything including exon labels. The exon labels can separately be adjusted relative to the base font size.
The coordinate label on the R-shiny app includes the gene, to make it clear when a new gene search results in a new coordinate range.
The scale_factor values are applied outside the memoise cache strategy, which should allow modifying the scale_factor values without invalidating the cache. It seems correct to cache the unadjusted data, then separately apply any adjustment.
The "farrisdata" package was added to the "Guides" tab which lists the versions of relevant packages.
The plot config side menu icon was changed from "wrench" to "gear", thanks to @DivadNojnarg of the "RinteRface/shinydashboardPlus" package on Github!
Updated R package dependencies for minimum versions for "shinydashboardPlus" and "farrisdata".

splicejam 0.0.47.900

In near future, sashimiAppConstants() may become the standard way to prepare the dependencies for sashimi plots, including the gene-transcript-exon models, the filesDF data.frame, the flattened exons, and color substitutions. This function will be able to take a GTF file, and prepare all the tx2geneDF cross-references, the exon and CDS exons, the flattened exons, using detectedTx if available for enhanced exon structures.
Package dependency on memoise, using Github version 1.1.0.9000 which allows invalidating a single problem cache file. It has been available since October 2018 but not released to CRAN yet. This changes is a step toward recovering from network outages, which currently create empty cache files which cannot be recovered without emptying the entire cache.

getGRcoverageFromBw() now checks if memoise cached data is NULL, which happens during network outage. If the data returned from the cache is NULL it clears the cache for that key, then tries again.
import_juncs_from_bed() now checks memoise cached data for NULL as described above.
sashimiAppConstants() was refactored, to define variables in a systematic way, by default updating global environment for convenience, but optionally creating a new environment inside which the required variables are populated. In future this technique may become the default here along with downstream functions, which may reference the environment rather than data objects themselves.

splicejam 0.0.46.900

Updated groups2contrasts() to detect when any factor level contains "-", and converts the "-" to "." prior to detecting contrasts. Previously the "-" interfered with proper contrast names, and resulted in some contrasts not being returned by this function. Note that this function avoids using base::make.names() because that function aggressively converts other valid characters to ".". However, if downstream functions require base::make.names() compliant names, run that function prior to calling groups2contrasts().
sortSamples() was updated to match "wildtype" as a control term.
groups2contrasts() was updated to check for specific scenarios where iFactors and iSamples may be missing, to cover a variety of common scenarios. Error messages were updated to be specific to the expected input.
flattenExonsBy() removed the ... dots argument, to try to appease the memoise caching logic, which is suspected to be comparing the ... data when invalidating the cached files. Ironically, this change itself will invalidate existing cached files.
internal_junc_score() was updated to handle data with no sampleColname column, which fixed an issue with the example code.
stackJunctions() was updated to handle multiple sample_id in the same operation, keeping each sample_id independent during stacking. This update should fix the edge cases where junctions appeared to be improperly stacked.
to_basic.GeomShape() is now exported, since it was causing problems during the call to plotly::ggplotly() when converting ggforce::geom_shape() to plotly format. Somehow it worked for the Sashimi coverage ggforce::geom_shape() but not for gene exon ggforce::geom_shape(). I am not always here to understand fully, but to make things work.

prepareSashimi() now returns list item "df" which contains the merged coordinates for coverage, junctions, and labels. This data.frame overrides the need for plotSashimi() to merge this data on the fly, and takes some extra logic away regarding junction rank, label positions, etc. It also returns "ref2c" as an attribute to the "df", to make sure it is available even when requesting only the "df" format. The "ref2c" contains the functions used to compress the introns on the x-axis scale.
plotSashimi() now expects the input sashimi object to contain list element named "df" to include the full coordinate data.frame used for plotting. Note that plotSashimi() will now require output from prepareSashimi() in version 46 or higher. Fortunately, memoise already invalidates the cache for even the slightest change in any molecule in the world, so caching should not be problematic.

splicejam 0.0.45.900

Made Sashimi plot the default tab. Fixed regression caused by page load with partially initialized input values.
Added aboutExtra as optional text to describe the data used in the R-shiny app.
Added R package versions to the Guides tab.
Added option to show legend in plotly interactive plots, which allows for some interesting filtering options, like hiding coverage, or junctions, or subsets of junctions based on predominance (.1 is minor, .2 is mixed, and .3 is major predominance.) Junction ranks are based upon having the highest score at each junction end, typically the predominant junction represents the predominant transcript isoform.

plotSashimi() new argument junc_alpha to control the alpha transparency of junctions, to allow transparency in cases where the intron coverage may be obscured by the junction arc.
Increased default minimum junction arc height from 100 to 200, the effect should be slightly higher junction arcs. In future, will consider inspecting intervening coverage max height as perhaps better estimate of a minimum junction arc, plus some buffer height.

splicejam 0.0.44.900

Fixed regression in R-shiny, updating the progress bar using gene in the caption, but the function did not need to know the gene.
Improved overall handling of reactive gene, sample_id values.

splicejam 0.0.43.900

plotSashimi() and gene2gg() have argument label_coords for optional x-axis range to subset labels before displaying with ggrepel::geom_text_repel(). This change solves the issue where zooming the x-axis range with coord_cartesian() kept all labels which were then arranged at the edges of the plot. This change also necessitates re-creating the ggplot object, since it has to change the label coordinate data.
Fixed some legacy code that assigned gene and sample_id to the global environment.
Removed the "Samples and Data" tab from R-shiny for now.
Improved level of detail in shiny progress bars, now shows each file being loaded. Not sure it is actually better than having less detail.
The order of sample_id items in R-shiny "Sample Selection" is now maintained, allowing custom sorting of samples.
Fixed error when junctions had no intervening junctions to use when determining the minimum height for a junction arc.
Fixed errors when part of the Sashimi plot data did not exist, for example no junction data or no coverage data.

splicejam 0.0.42.900

prepareSashimiData() argument use_memoise enables memoise caching of individual bigWig files per gene, and individual junction files per gene. The file paths are defined by memoise_coverage_path and memoise_junction_path. These options should greatly enhance the success rate of caching, at the expense of creating more cache files.
getGRcoverageFromBw() now has arguments use_memoise and memoise_coverage_path to cache at the level of each bigWig file and genomic range.
R-shiny by default caches sashimi data, so repeated calls for the same gene and same set of sample_id will retrieve the full cached sashimi data. However, if any smaller argument changes, including changes to any bigWig coverage or junction BED file, each individual step is also cached to prevent retrieving the same coverage or junction data repeatedly. For practical R-shiny usage, where sample_id is frequently changed, this update should be a substantial improvement.
Changed default R-shiny to non-interactive. One day will switch it back, but need plotly ninja skills meanwhile.

splicejam 0.0.41.900

Changed sashimiAppConstants() to improve handling of memoise flatExonsByTx data.
Updated the Guides tab with a description of Sashimi plots, and a how-to for creating a Sashimi plot.

splicejam 0.0.40.900

Added shinyjs package dependency.

splicejam 0.0.39.900

Fixed regression in junction scale factors, not consistently applied in prepareSashimi().

splicejam 0.0.38.900

Dependency added for shinyjqui to use orderInput() for drag-and-drop selection and ordering of sample_id values.
Dependency added for shinycssloaders.

New tab "Sample Selection" which focuses on selecting and ordering the unique sample_id entries found in filesDF.
"Samples and Data" tab allows editing columns, and will include updated "scale_factor" values in normalizing coverage and junction scores.
"Samples and Data" tab uses color_sub to colorize the table, and will create colors for any undefined values in the "sample_id" column. Other columns are colorized when all values match names(color_sub) otherwise are not colorized. Columns are arranged so any extra columns (such as group, subgroup, batch, etc.) would appear beside sample_id, and typically would be colorized also using color_sub.
Added spinning loader indicator to the plot panel, which covers the time after data is prepared, but before ggplot has created the actual visualization.
The "Sample Selection" tab now allows setting the number of plot panel columns. However, it breaks the synchrony with the gene-exon model, since the gene panel is still full-width. Already thinking of alternatives.
Plot settings like panel height, font relative sizing, and exon label size (for non-interactive) are available.

splicejam 0.0.37.900

Added panel height to R-shiny UI, controlling the allocated height for each facet panel.
Numerous updates to the plotly highlighting methods.
Reorganized the R-shiny UI, still in progress.
Added R-shiny tab "Sample and Data" intended to customize and select sample_id entries to display or hide in the Sashimi plots. Purely aesthetic and non-functional, still testing out the many javascript table options available.

splicejam 0.0.36.900

Fixed regression in use of color_sub to pre-define categorical colors in sashimi plots.
Updated plotly highlighting, increasing the success rate in most test cases.

splicejam 0.0.35.900

grl2df() now returns seqnames, and adjusts yBaseline within each seqname (chromosome). To plot multi-chromosome GRangesList, use +facet_wrap(~seqnames)
R-shiny enabled some plotly highlighting features, currently in testing phases.
Major refactor of plotSashimi() to merge together the junction, coverage, and label coordinate data.frames to enable plotly and crosstalk to highlight features. The end result looks amazing.

splicejam 0.0.34.900

R-shiny new options: minimum junctions; show by strand.
R-shiny now defines each to the global environment if they do not already exists: exonsByTx, cdsByTx, flatExonsByGene, flatExonsByTx, tx2geneDF, detectedTx, detectedGenes. This mechanism is used for now, both to help define custom input data, but also to help define the data values needed to produce plots manually outside R-shiny.

splicejam 0.0.33.900

stackJunctions() now also returns "junction_rank" scored from 1 to 3, where 1=minor, 2=partial, 3=major, based upon the rank of junctions entering and leaving exons.
Junctions are drawn in order from dominant to minor, which has the effect of ensuring smaller junctions are displayed. The junc_fill is converted to gradient so a darker color is used for dominant junctions, to try to highlight the major isoform splice junctions per sample. Unfortunately, plotly does not honor the polygon render order (yet).

splicejam 0.0.32.900

Added flatExonsByTx to R-shiny app, to be able to display transcript isoform exon structures alongside the flattened gene-exon model.
Added R-shiny option to display transcript isoforms alongside the gene-exon model. Also option to show all or detected transcripts.

splicejam 0.0.31.900

Splice junctions now require at least one junction end within the range being displayed, to avoid junctions that do not connect with the visible gene model.
The x-axis range of multiple plots are more consistently controlled, to avoid one panel autoscaling to display a wider junction than other panels.

Plotly views contain custom tooltip text, using the sample_id, the name of the exon or feature, and the track (referring to the name of the coverage).

splicejam 0.0.30.900

New ggplot2 geom geom_diagonal_wide_arc(), extends ggforce::geom_diagonal_wide() by connecting the left and right halves of a diagonal into one continuous ribbon arc.

plotSashimi() now uses geom_diagonal_wide_arc() to display junction arcs instead of using two ggforce::geom_diagonal_wide(). For now, prepareSashimi() still provides coordinates to create two polygons, which are combined in the geom. Still todo: figure out how to add a label; and make the middle x position immune to x-axis rescaling.

splicejam 0.0.29.900

R-shiny app now properly keeps interactive plot x-axis ranges in sync, when zooming the plot.
Fixed bug in prepareSashimi() that occurred when no junctions overlapped another, resulting in error "invalid 'type' (S4) of argument".

splicejam 0.0.28.900

defineDetectedTx() has a new argument zeroAsNA to handle the special case where some expression values reported as zero should be treated as NA (no data obtained) and therefore will not be included in group mean calculations. As transcript-exon models get more "comprehensive", kmer quantitation tools such as Salmon and Kallisto sometimes need to assign abundance to one of several nearly identical isoforms, and in low count scenarios all counts may be assigned to one or another isoform, leaving zero in the alternate position. Excluding zero ensures that group mean values represent only the assigned quantitation.

splicejam 0.0.27.900

Packages now imported for launchSashimiApp(): shiny, shinydashboard, shinydashboardPlus, shinyWidgets.
getGRcoverageFromBw() now returns NULL when a BigWig file is not accessible. Previously any error caused "Error in seqinfo(con) : UCSC library operation failed" which could mean the file does not exist, or any number of other validation checks failed. Since getGRcoverageFromBw() used a vector of BigWig files, any error caused the entire set to fail.
getFirstStrandedFromGRL() added package prefix to the use of IRanges::heads() which was not imported directly.

R-shiny plots now set the plot height for ggplot2 or plotly, depending upon the number of samples, and presence of gene-exon model. Future versions will allow R-shiny user customization.
bgaPlotly3d() removed some unnecessary print functions.

splicejam 0.0.26.900

This version is an incremental update, while we evaluate some display options of Sashimi plots in the R-shiny app.
Minor aesthetic changes to R-shiny app, including plotly interactive options, and evaluating some UI elements in sidebar.
Added option to display gene-exon model in R-shiny.

splicejam 0.0.25.900

makeTx2geneFromGtf() help docs recommend installing the R.utils package when .gz files are required for import, since this process uses data.table::fread().
Package dependencies were added for shiny, shinydashboard.

to_basic.GeomShape() is a hidden function intended only to provide basic support of ggforce::geom_shape() when converting ggplot objects to plotly.

splicejam 0.0.24.900

R-shiny Sashimi app now allows zooming into coordinate ranges, defined per gene.

splicejam 0.0.23.900

First working Sashimi R-shiny app, still has issues with certain genes that needs debugging. Defaults to using Farris et al data from farrisdata package, but can be overridden with global environment variables.

splicejam 0.0.22.900

Initial R-shiny launchSashimiApp() function.
Suggests the farrisdata package for example data used for the Farris et all RNA-seq mouse hippocampus manuscript.

splicejam 0.0.21.900

Fixed examples that did not explicitly call library() for required libraries.
Fixed error in codonUsage2df() example data file path.

Added specific TODO items.
Added two function categories: "jam ALE-specific RNA-seq functions", and "jam codon-usage RNA-seq functions" to help organize the large list of accessory functions.

splicejam 0.0.20.900

Minor fixes to examples.

Added data test_exon_gr, test_junc_gr, test_cov_gr for easy example data for exons, junctions, and coverage, respectively.
Added "wide" variants of the above test data, with introns about 100x larger than exons, consistent with mammalian gene structures.
Added examples to each data, showing how one would use the raw data to generate different visualizations used in Sashimi plots.
Added sample data to the vignettes and some examples.
Renamed flattenExonsByGene() to flattenExonsBy() to reflect that the function handles by="gene" and by="tx".

splicejam 0.0.19.900

Added create-a-sashimi-plot.Rmd which walks through a full example showing how to create a Sashimi plot.
Added examples to stackJunctions() with schematics, including example on plotting junctions by themselves.

Removed compressGRgaps() for now, since the methods now try to keep GRanges intact, and instead transform the x-axis scale to compress visible gaps.

splicejam 0.0.18.900

bgaPlotly3d() now properly handles ellipsoid colors, previously the colors were assigned but not honored by plotly::add_trace().
combineGRcoverage() determines strandedness by requiring all values to be at or below zero, with at least one negative value. Otherwise, data can have position and negative values and will be considered positive stranded.
plotSashimi() replaces jamSashimi() because it is just more intuitive... Ah well.
Fixed small typo in plotSashimi.Rd help that included an unmatched quote.

splicejam 0.0.17.900

jamSashimi() is used to plot Sashimi data prepared by prepareSashimi() in order to separate the download and preparation of Sashimi data from the visualization.

prepareSashimi() is refactored to remove the plot functions, moving them to the new jamSashimi().
flattenExonsByGene() can now handle Tx data, mainly useful to add CDS regions to existing exon models.
gene2gg() is more robust to edge input cases.

splicejam 0.0.16.900

prepareSashimi() is a workhorse function that prepares several types of Sashimi-like data output, including ggplot2-based Sashimi plots. This plot uses vanilla ggplot2 with custom x-axis scaling to compress genomic coordinates, while keeping data in proper genomic coordinate space.
gene2gg() is a lightweight function that creates gene and transcript exons models, and returns a ggplot2 object for plotting. It can optionally return the data.frame used by ggplot2.
grl2df() is similar to fortify() from ggplot2, or the broom::tidy() functions, that take a custom object and return a data.frame for downstream use. Here the function currently works with "rectangle" data (like exons, introns, peaks, etc.), and "junction" (like junction regions to be represented by ggforce::geom_diagonal_wide()). In future it may also handle sequence coverage polygons.
exoncov2polygon() converts a GRanges object containing coverage in the form of NumericList for each exon or intron, into a data.frame suitable for use by geom_polygon() or ggforce::geom_shape().
getGRcoverageFromBw() loads bigWig coverage data for a GRanges of exons and introns, returning a GRanges object with columns representing each sample_id. It calls combineGRcoverage() to combine coverages by strand within each sample_id.
flattenExonsByGene() is intended to provide a set of unique exons per gene, using all or only detected transcript exon models. It numbers exons by contiguous segment, then labels subsections of each exon with a letter suffix, for example "exon1", "exon2a", "exon2b", "exon3". Lastly, it can annotate exons as CDS or non-CDS, if given a set of cdsByTx data.
make_ref2compressed() takes a GRanges object of exons (or any useful feature like ChIP-seq peaks, etc) and returns functions needed to compress x-axis coordinates, in order to shrink gaps/introns to a fixed width, suitable for use by ggplot2.
spliceGR2junctionDF() takes junctions GRanges data, and flatExonsByGene, and summarizes and annotates each junction by the gene_exon connected, and combines scores when multiple junctions are within "spliceBuffer" distance of an exon boundary, by default 3 bases. It can accept a GRanges object that was derived from multiple sample_id, and will return data summarized within each sample_id. It calls stackJunctions() to combine junctions per replicate.
simplifyXY() takes a vector of coordinates, and simplifies them to the minimal set of points to represent the polygon. For sequence coverage data, that process can reduce individual points by 90%, but it works with any coordinate data. When two or more consecutive line segments have identical angle (with non-zero distance), they are combined using only the first and last points.
getGRgaps(), getGRLgaps(), addGRgaps(), addGRLgaps() are functions that take GRanges input, and return either just the gaps between non-overlapping regions, or the original features with gaps inserted between them. Useful to convert a set of exons, to a set of exons and introns.

Added package dependencies to ggplot2, ggforce, ggrepel

Need a way of annotating GRangesList gaps by the parent feature name.
In future, allow samples to have replicates, optionally allow each replicate to be independently plotted, while being part of the parent sample_id.
Allow alternative input for prepareSashimi(), namely BAM alignment files, from which coverage and junctions can be derived.
Consider making ref2c chromosome-wide, however it would require x-axis coordinates to know their context, in terms of chromosome/seqname.
Multiple vignettes to demonstrate workflows: Sashimi plots; preparing exon GRangesList; using annotateGRLfromGRL() to add annotations, etc.

splicejam 0.0.15.900

curateVtoDF(), curateDFtoDF() are data curation functions to curate a vector, or a data.frame, into a data.frame with consistent, usable nomenclature for downstream analysis. They use a flexible yaml format that should help automate analysis pipelines that start with raw data file import.
exoncov2polygon() and compressPolygonM() are basic functions for sashimi plots, efficiently converting exon/intron coverages to multi-polygons, then optionally compressing introns and reducing the information content to roughly similar resolution as uncompressed regions.
spliceGR2junctionDF() is the summary function to convert a set of splice junction read counts to gene-annotated junctions, grouped and summed where needed.
closestExonToJunctions() called by spliceGR2junctionDF() is used to annotate junction ends near compatible exon boundaries, with some buffer distance allowed to "snap" junctions to the edge.

splicejam 0.0.14.900

Fixed issue where numTxs was not getting populated in runDiffSplice(), otherwise the stats summary is not changed.

splicejam 0.0.13.900

Added "openxlsx" to Suggests, for exporting Rmarkdown stats tables to Excel format.
runDiffSplice() includes examples using groups2contrasts(), also allows txColname,geneColname to be defined and therefore custom.
Changed all verbose=TRUE to verbose=FALSE by default.
Changed makeTx2geneFromGtf() to use data.table::fread() ability to uncompress .gz files, hopefully making it cross-platform.
groups2contrasts() was updated to handle single-factor experiments, and be more robust to two-factor experiments with missing groups in the full design table.

Added basic RNA-seq workflow to vignettes.

splicejam 0.0.12.900

runDiffSplice() is a wrapped around limma::diffSplice() intended to capture several steps of pre- and post-processing, optionally applying limma::voom().
groups2contrasts() takes a vector or data.frame of sample groups, and determines the relevant pairwise and two-way contrasts, returning a design matrix and contrast matrix.
sortSamples() sorts biological samples so that known patterns of control group terms are returned before non-control groups, in order to help provide useful defaults when setting up sample group contrasts.
strsplitOrdered() provides base::strsplit() but returns factor output whose factor levels are influenced either by factor input, or by other arguments.

limma package was added to Imports.
runDiffSplice() has an argument spliceTest which defines test when calling limma::topSplice(). Only the "t" (t-test) returns fold change, therefore hits are not filtered by fold change for "F" or "simes".

splicejam 0.0.11.900

ale2violin() takes output from tx2ale() with some arguments, and produces a ggplot2 violin plot object, as well as the underlying data. It allows a custom filtering function, which allows filtering gene lists for relevant regions of expression.

splicejam 0.0.10.900

shrinkMatrix() minor fix to remove the shadow x in the resulting colnames.
tx2ale() modified to be tolerant of NA values in the expression matrix.

splicejam 0.0.9.900

sortGRL() sorts GRangesList objects by chromosome and position.
getFirstStrandedFromGRL() return the first GRanges feature per GRangesList, ordered properly by strand.
annotateGRfromGR() which annotates one GRanges object based upon overlaps with another GRanges object.
annotateGRLfromGRL() which annotates one GRangesList object based upon overlaps only with the same index entries in a second GRangesList object.
findOverlapsGRL() runs GenomicRanges::findOverlaps() for the case of two GRangesList objects, matching at the GRanges level but restricting overlaps to those matching the same GRangesList index.
assignGRLexonNames() assigns exon names and numbers to a disjoint set of exons per gene model.

Added "S4Vectors" to package imports, since some functions like lengths() have been moved there. Another reason using a package prefix is clunky at best. If methods have dispatch, and if they did not conflict between S3 and S4 methods, that would be the better strategy. It is not a solution to hardcode package names into function bodies, since every package maintainer has to stay updated on the source package of all other dependent functions. Those details should be irrelevant to other package maintainers.

splicejam 0.0.8.900

The "arules" package was moved to "Imports" since it is required for the list2im() function. A slower workaround could be written, but ultimately the arules package is preferred.
Configured the package to use pkgdown for function references.
Added "#' @imports jamba" to import all jamba R functions.

splicejam 0.0.7.900

factor2label() will convert a factor to a factor label, with the same order of levels as the input factor, but including summary stats like the number of items for each factor level. Useful for ggplot2 visualizations, to include counts in the color legend for example.

splicejam 0.0.6.900

Added reference file "Mouse_codon_usage.txt" to the "extdata" folder, as example input both for farrisSeq.Rmd, and for other species. Access the file path with this command: system.file("extdata", "Mouse_codon_usage.txt", package="farrisdata")

codonUsage2df() imports a text codon usage file, and returns a data.frame. Support function dna2codon() simply takes a character vector and returns vector whose elements all have three characters, e.g. all(nchar(x) == 3).
Two geometric mean functions: jamGeomean() is preferred by the Jam packages, but geomean() is provided for direct comparison to the classical approach.
detectedTxInfo() summarizes the data used to define detected transcripts for a given gene, or for a given set of transcripts.

splicejam 0.0.5.900

Minor fix to makeTx2geneFromGtf() to remove requirement for col.names during import.
Several minor documentation updates.

splicejam 0.0.4.900

Updated the DESCRIPTION file to include proper "Remotes" entries and depencies for jamba, colorjam, and jamma packages.
Fixed issue where the data.table package required a specific #' @import data.table entry in the roxygen2 entry for the shrinkMatrix function. This issue prevented defineDetectedTx() from working within an R package.

defineDetectedTx() is a core RNA-seq function to determine which transcript isoforms are considered "detected" based upon counts (or pseudocounts), TPM values if available, and the relative abundance of isoforms per gene. When "everything with over 10 counts" is not sufficient.
tx2ale() takes a set of transcript exon models, and returns a set of alternate 3'UTR regions, similar to ALE (alternative last exon.) It differs slightly from other methods in that it aggregates transcript quantities by shared ALE regions, producing a matrix based upon unique ALEs. It does not use counts in the ALE region itself, but the aggregate abundance of all isoforms that contain each ALE. This method allows tools like Salmon or Kallisto to quantify isoforms using the best available kmers per isoform, without being restricted to the ALE regions which have a very wide distribution of lengths.
makeTx2geneFromGtf() takes a GTF file, and produces a data.frame with tx (transcript) to gene associations.

list2im() converts a list to an incidence matrix. It uses the arules package fast methods for creating transactions objects, which are sparse binary matrices with linked data.frames used to describe rows and columns. Similar to SummarizedExperiment but with optimization specifically for list-to-matrix and matrix-to-list conversion. Their implementation is memory efficient as well.
bgaPlotly3d() takes a "bga" class, as produced by the made4::bga() function, and produces a 3-D plotly visualization. It adds ability to group centroids into "supergroups" which are connected by a spline 3-D curve.
spline3d() is the supporting function to draw interpolated 3-D curves through a set of coordinates.
shrinkMatrix() shrinks a numeric matrix by groups of rows, essentially a wrapper function for the data.table package functions.

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.

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jmw86069/splicejam Analysis and Visualization of Gene Splice Variants and Transcriptome Data

NEWS.md In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

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jmw86069/splicejam
Analysis and Visualization of Gene Splice Variants and Transcriptome Data

NEWS.md
In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data