To update IMGTStatClonotype' R package, you can follow steps described here.
Where can I find the 'stats_xxx' files for IMGT/StatClonotype inputs?
IMGT/StatClonotype works only with uploaded files (.txt format) from the IMGT/HighV-QUEST statistical analysis output ('stats_xxx' file available in 'data' directory of the IMGT/HighV-QUEST statistical analysis output where 'xxx' is the batch name and the locus type)
The files uploaded (for set 1 and set 2) in IMGT/StatClonotype should have 26 columns:
"cdr3aa", "expid", "clonoIndex", "onecopy", "morethanone", "total", "indexes", "vgene", "vallele", "dgene", "dallele", "jgene", "jallele", "cdr1", "cdr2", "gcdr1", "gcdr2", "pid", "length", "c104", "f118", "anchors", "seqid", "functionality", "sequenceFileNumber", "sequenceClonoFileNumber".
You can find files examples here.
Why, for my two sets, the tab 'CDR-IMGT AA properties' shows bar graphs of the common 20 amino acids at only 4 positions within the CDR3-IMGT, and each position shows only 1 amino acid?
The smallest length found in each of the two sets is selected by default in the left sidebar. If there is one sequence in one or both of the two sets having a CDR3-IMGT of length 4 (smallest length), the bar graph shows the amino acid found at each of the 4 positions.
Other CDR3-IMGT lengths can be selected in the sidebar 'CDR3-IMGT length selection (set 1)' and 'CDR3-IMGT length selection (set 2)'. New graphs with several amino acids will be displayed if there are several sequences with the lengths selected for each set. .
Why the message 'NA/NaN argument' appears in the interface of the tab 'CDR-IMGT AA properties'? Is it an issue?
The error message 'NA/NaN argument' can appear in the interface for few seconds when you click on the panel "CDR-IMGT AA properties" just after uploading the two sets because the list of CDR-IMGT lengths is empty while the program is in the process of recovering it for the first time.
I get some warning messages in the R console like [Warning in origRenderFunc(): Ignoring explicitly provided widget ID...]. Is it an issue?
Some warning messages, added by other R package developers, can appear in the R console and it should be safe to ignore them and this cannot affect the obtained results.