BoxPlot.metabolism issue, obj not in function code

[msalaciak]

I noticed BoxPlot wasn't working, couldn't find countexp.Seurat

Turns out in the function, the Countexp.Seurat was not replaced by parameter = obj

scMetabolism/R/visualize_metabolism.R

Lines 174 to 180 in 9b79b07

	BoxPlot.metabolism <- function(obj, pathway, phenotype, ncol = 1){
	input.pathway<-pathway
	input.parameter<-phenotype
	metadata<-countexp.Seurat@meta.data
	metabolism.matrix <- countexp.Seurat@assays$METABOLISM$score

[wu-yc]

Hi Salaciak,

Thanks for your comment. We are now working on it and will revise the code ASAP

[xutongran]

Hi Wu yc !
I had a similar problem, when i run this command "DotPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", norm = "y")", Error in [.data.frame(metadata, , input.parameter) : 选择了未定义的列, I want to request you: how to fix this kind of error

[kake1998]

Why can't you install this package?

[sergio-rutella]

The boxplot issue has not been resolved yet. I am working with this package now and I keep getting the same error!

[msalaciak]

@sergio-rutella What I did to fix it is I just copied the entire function from here and just changed all instances of Seurat to the parameter obj and it works!

scMetabolism/R/visualize_metabolism.R

Lines 174 to 210 in 9b79b07

	BoxPlot.metabolism <- function(obj, pathway, phenotype, ncol = 1){
	input.pathway<-pathway
	input.parameter<-phenotype
	metadata<-countexp.Seurat@meta.data
	metabolism.matrix <- countexp.Seurat@assays$METABOLISM$score
	metadata[,input.parameter]<-as.character(metadata[,input.parameter])
	metabolism.matrix_sub<-t(metabolism.matrix[input.pathway,])
	#arrange large table
	gg_table<-c()
	for (i in 1:length(input.pathway)){
	gg_table<-rbind(gg_table, cbind(metadata[,input.parameter], input.pathway[i], metabolism.matrix_sub[,i]))
	}
	gg_table<-data.frame(gg_table)
	gg_table[,3]<-as.numeric(as.character(gg_table[,3]))
	library(wesanderson)
	pal <- wes_palette("Zissou1", 100, type = "continuous")
	ggplot(data=gg_table, aes(x=gg_table[,1], y=gg_table[,3], fill = gg_table[,1])) +
	geom_boxplot(outlier.shape=NA)+
	ylab("Metabolic Pathway")+
	xlab(input.parameter)+
	theme_bw()+theme(axis.text.x = element_text(angle = 45, hjust = 1), #aspect.ratio=1,
	panel.grid.minor = element_blank(), panel.grid.major = element_blank()) +
	#scale_color_gradientn(colours = pal) +
	facet_wrap(~gg_table[,2], ncol = ncol, scales = "free") +
	labs(fill = input.parameter) +
	#theme_bw()+theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
	NULL
	}