[R] unable to carry through object in a nested function

[arun]

Hi,
Try this:
GetPropPlot<- function (PrePropData, direction, SSThreshold, cell, stim) {
       if (direction== ">") {
        PropData<-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY), here(summarise),
            PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
        }
    PlotSubset <- subset(PropData, STIM==stim & CELL == cell)
    FinalPropPlot<-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
        geom_line() +
        geom_point() +
        facet_grid(SIGNAL~SUBJECT)
    return(FinalPropPlot)
    }


GetPropPlot(PrePropData, direction=">", SSThreshold=3, "CD4", "No")
A.K.


On Wednesday, January 22, 2014 10:51 PM, "Chen, George" <George.Chen at roswellpark.org> wrote:
Hi,
This is a resend of a previous message reproduced below but with sample data to run.
Thanks.
George Chen



Hi There,
I am having trouble carrying through an object listed in the outer function into the inner function of a nested pair.

--------sample data below ---------
library(plyr)

SUBJECT<-c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
STIM<-c("No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No","No")
CELL<-c("CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4","CD4")
SIGNAL<-c("ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC")
DAY<-c(7,7,7,7,7,7,7,7,7,7,1,1,1,1,1,1,1,1,1,1)
SIMSCORE<-c(2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5)
PrePropData<-data.frame(SUBJECT, STIM, CELL, SIGNAL, DAY, SIMSCORE)
________________________________


This is my code:

FindGreaterThanProportion<- function (y, SSThreshold) {
    DenomCells<-length(y)
    NumerCells<-subset(y,y>SSThreshold)
    PropCells<-length(NumerCells)/DenomCells
    return (PropCells)
    }


GetPropPlot<- function (PrePropData, direction, SSThreshold, cell, stim) {
    # Split up the dataframe with ddply and apply the function
    print(direction)
    print (SSThreshold)

    if (direction==">") {
        PropData<-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY), summarise,
            PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
        }

    PlotSubset <- subset(PropData, PropData$STIM==stim & PropData$CELL == cell)
    PropPlot<-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
        geom_line() +
        geom_point() +
        facet_grid(SIGNAL~SUBJECT)
    return(FinalPropPlot)
    }

GetPropPlot(PrePropData, direction=">", SSThreshold=3, "CD4", "No")

When I run the code, I get this error:
[1] ">"
[1] 3

Error in subset.default(y, y > SSThreshold) :
  object 'SSThreshold' not found

It seems as if SSThreshold is not being passed into FindGreaterThanProportion.

Any help would be appreciated to determine what I am doing incorrectly.
Thanks in advance.

George Chen



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