Undefined columns error R cytometry analysis
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Elizabeth • 0
@df46ae5a
Last seen 5 months ago
United States

Enter the body of text here

Hello! I have been following the GvHD code in order to work on analyzing flow data in R. However, I keep getting the following undefined columns error Code should be placed in three backticks as shown below

knitr::opts_chunk\$set(echo = TRUE)
library(ggfortify)
library("flowCore")
library("mtvnorm")
library(ggcyto)
library("ggplot2")
library(flowWorkspace)
library(flowWorkspaceData)
library(xtable)
library(cowplot)

gs@transformation <- transform(colnames(gs)[-(1:2)], flowjo_biexp_trans())

autoplot(gs[1], gate = c("CD3","CD19"), bins = 64) +
geom_overlay(data = "IgD+CD27+",size=0.25)

Error in [.data.frame(x@transformation, i) : undefined columns selected


Any help would be appreciated thanks.

flowCore ggcyto FlowCytometryData • 187 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 19 days ago

I see you are trying to fill the missing transform info to gs_bcell_auto , which is a hack, but since you seems to know what you are doing, here is the right way of doing it (still a hack though)

tranlist = transformerList(colnames(gs)[-(1:2)], flowjo_biexp_trans())
gs@transformation <- sapply(sampleNames(gs), function(i)tranlist, simplify = F)