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Suggestion from annual satisfaction survey:
"Pouvoir extraire les logFC mais aussi les p-values et les p-values corrigées à partir des sous-groupes de gènes identifiés dans un cluster "
-> add logFC and Pval to the "Table summarizing the heatmap" in "Clusters" tab of Heatmap Menu.

names of export push buttons are inverted in volcano page
solution: revert the names of export buttons

Il serait bien qu'il y ait la possibilité de choisir parmi toutes les couleurs possibles afin d'obtenir des figure cohérentes avec nos résultats obtenus via d'autre logiciel

when on wants to save a volcano to eps file, it exports the last plot generated (barplot).
Origin: /module/savemodules.R:L#116
Cause: ggsave by default save the lsat plot object generated, so the barplot if it is generated.
Solution: change the use of command ggsave() to cairo_ps()

in stripchart, enlarge pvalue criteria to have the possibility to highlight non regulated genes.

here the strategy:
https://string-db.org/help//api/#embedding-the-interactive-network

integration to shiny:
https://stackoverflow.com/questions/60492135/string-interactive-network-in-shiny-in-r
https://www.semicolonworld.com/question/66144/string-interactive-network-in-shiny-in-r

confusion in y axis name. Data are log2 expression values.
Solution: rename yaxis to "log2 expression"

when sending gene list from heatmap to enricher this gives a blank page with this content:
{
"expired": true
}

sampleNames are renamed to get only numbers, pasted with groupName. this can generate duplicated sampleNames and ERROR.
Solution: Disable sample name renaming

some files are not necessary for the app to run.
final

the FC treshold in volcano plot is based on log2FC.
Correct this to be based on FC
->file function/EnhancedVolcano.R

Review the Functional analysis widget of Heatmap:
line 1: Organism[list]; category[list]
line 2: Run Enrichment Analysis[buton]; with DAVID WS[text]
line 3: Send to DAVID[button]; Cluster[list]

Sometimes, ResTables can contain NA values in FC, pvalues... and causes error in summary table, stripChart and heatmap.
2 possible solutions:
Choice 1 - manage NA values in summary page, heatmapand StripChart filtering criteria.
Choice 2 - filter out lines with NA after data loading

got this msg:
Due to the ambiguous nature of gene symbols, DAVID does not allow their upload with the API at this time.
We are currently developing methods to submit a taxonomy id with an api call for OFFICIAL_GENE_SYMBOL.
Please Contact Us if you have any questions.

-> update the kind of gene identifiers used for the request

data stored in grouplength object (server/HeatmapHiny.R).
solution: transform rowname to column.