In sportiellomike/fluximplied2: Pathway analysis software utilizing rate limiting steps

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

# download fluximplied from github
# if you're reading this, you probably already have, so I've commented out all these steps.
# you may have to install devtools with the below code: 
# install.packages("devtools")
# library(devtools)
# install_github('sportiellomike/fluximplied@dev',build_vignettes=T)
library(fluximplied)

# Let's use the exampleData included in this package
head(exampleData)
# as you can see, it has genes that are not related to metabolism, genes that are, and some genes that are that are also rate limiting steps. 

# Let's also make an example set of data where none of the genes have a padj below 0.05
exampleDatawithoutsignificantRLSs<-exampleData
exampleDatawithoutsignificantRLSs$padj<-0.051

# let's load the parameters for fluximplied
inputdat<-exampleData
inputformat='df'
species="mmu"
geneformat="SYMBOL"
padjcolname='padj'
LFCcolname= 'log2FoldChange'
pcutoff=0.05

# now actually run fluximplied
fluximplied(inputdat = inputdat,
            geneformat=geneformat,
            species = species,
            padjcolname = padjcolname,
            inputformat = inputformat,
            LFCcolname = LFCcolname,
            pcutoff = pcutoff)

# And let's do the same thing but with our example dataset that doesn't have any significant Padj values.
inputdat<-exampleDatawithoutsignificantRLSs
inputformat='df'
species="mmu"
geneformat="SYMBOL"
padjcolname='padj'
LFCcolname= 'log2FoldChange'
pcutoff=0.05

# now actually run fluximplied (uncomment it if you want it to run)

# fluximplied(inputdat = inputdat,
#             geneformat=geneformat,
#             species = species,
#             padjcolname = padjcolname,
#             inputformat = inputformat,
#             LFCcolname = LFCcolname,
#             pcutoff = pcutoff)

# let's reset our parameters to the original ones including using our dataset with significant Padj values.
inputdat<-exampleData
inputformat='df'
species="mmu"
geneformat="SYMBOL"
padjcolname='padj'
LFCcolname= 'log2FoldChange'
pcutoff=0.05

# You can also change the title and any other part of the plot using standard ggplot functions
fluximpliedplot+
  ggtitle('hello world')+
  theme_dark()+
  theme(plot.title = element_text(hjust = 0.5))+
  scale_fill_gradient2() 

# Here is an example with a character vector of genes.
inputdat<-c('Cpt1a','Ifng','Tnf','Pfkl')
inputformat<-'vector'
fluximplied(inputdat = inputdat,
            geneformat=geneformat,
            species = species,
            padjcolname = padjcolname,
            inputformat = inputformat,
            LFCcolname = LFCcolname,
            pcutoff = pcutoff)

###FIN###

# session_info()

sportiellomike/fluximplied2 documentation built on Jan. 30, 2024, 12:47 p.m.