nthomascube / traitcorr

traitCorr (v0.8)

TraitCorr - correlating gene expression with phenotypic data

The user interface TraitCorr allows to determine those genes that significantly correlate with a selected trait or among traits and provides various visualisation and analysis possibilities.

Screenshots of the tool

correlation of transcriptome data with trait information

Literature

Please find our manuscript published in Gene Reports TraitCorr-Gene-Report-Nussbaumer et al. 2020 and our preprint TraitCorr-Preprint-Nussbaumer et al., 2019

Installation

Following packages are needed, the Rscript "ReporteRs" has been replaced by R package "officer", as suggestd by davidgohel/ReporteRs.

library(d3heatmap)
library(gplots)
library(officer)
library(VennDiagram)
library(scales)
library(shiny)
library(shinyalert)
library(shinyBS)
library(shinyjs)
library(shinythemes)
library(xlsx)

This is how to run it:

source("methods.R")
source("ui.R")
source("server.R")
shinyApp(ui,server)

To simplify the process of running traitcorr we added the method run_traitcorr that includes all dependencies.

Normally, I would copy the content of run_traitCorr.R into the R workbench and then I first see whether R packages are still needed. If so, then the R shiny GUI should be displayed. The input_data "traitCorr_input.zip" would have to get extracted and finally the data can be included and afterwards possible to analyse the demo files.

run_traitcorr()

traitcorr's Issues

Error: "unable to find an inherited method for function"

Hello! How are you doing?

I tried to run traitCorr, but I've had some problems.

When I run source("run_traitCorr.R"), this message comes up: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘print’ for signature ‘"character"’, and I can't even choose an input file.

If I run:
source("methods.R")
source("ui.R")
source("server.R")
shinyApp(ui,server)
The pop up appears, but as soon as I choose an input file, the following message comes up: Listening on http://127.0.0.1:3355 Warning: Error in <Anonymous>: unable to find an inherited method for function ‘print’ for signature ‘"character"’ [No stack trace available]

Finally, if do as mentioned in the second example, but chose the option of running it on my browser, I can choose an input file, but just one. After I choose it, the screen freezes, and I can't continue.

Do you know how I shoul proceed?

Thanks in advance!

Best,
Pedro Martins