R/graph_table.R

In peterwu19881230/microbialPhenotypes: Tools That Analyze Phenotypic Profiles by Annotation Sets

graph_table <-
function(table){
    if(!(class(table) %in% c("matrix","data.frame","data.table"))) stop("Input is not a matrix, data frame or data table")
    
    #summarize the table if it contains only numbers
    if(class(table)=="matrix" && typeof(table) %in% c("integer","single","double")){
        table[]=sapply(table,FUN=function(point)as.numeric(point)) # [] is to preserve the structure of the matrix/data frame/data table
        print("From all data in the table"); print(summary(as.numeric(table))) #Note: most numbers (including 1,2,3...) are represented as double by default in R
    }else table[]=sapply(table,FUN=function(point)as.numeric(point)) 
    
    #Remove the names so they don't get plotted
    colnames(table)=NULL
    rownames(table)=NULL
    
    
    #Check to see if required packages have to be installed
    #Ref: https://stackoverflow.com/questions/4090169/elegant-way-to-check-for-missing-packages-and-install-them
    listOfPackages=c("grid", "pheatmap")
    new_pack=listOfPackages[!(listOfPackages %in% installed.packages()[,"Package"])]
    if(length(new_pack)){
        print(paste(new_pack," is required and being installed...",sep=""))
        install.packages(new_pack)
    } 
    
    
    #Reset the range for colors: middle color: median, color range: lower-upper 
    #(This way the breaks below median and above median are not equal, but it should be fine)
    q=quantile(table,na.rm=T); q1=q["25%"]; med=q["50%"]; q3=q["75%"]; iqr=q3-q1
    lower=q1-3*iqr
    upper=q3+3*iqr
    palette.breaks=c(0:50*(med-lower)/50+lower,1:50*(upper-med)/50+med) #Sometimes (eg. when inputting ternary data) there will be this issue: 'breaks' are not unique. Have to fix
    
    ##print it
    pheatmap::pheatmap(table,cluster_rows=F,cluster_cols=F,breaks=palette.breaks,show_rownames =F, show_colnames = F)
}