Error while plotting in ggplot2
1
1
Entering edit mode
19 months ago

Hi,

I am trying to the plot the grid plot using the ggplot2 library, however, I am getting the error as given below. Please assist me with this.

Error in `[.data.frame`(Group_plot, , virus_strain) : 
  undefined columns selected

Thank you,

Toufiq

EDIT by @RamRS:

OP edited their question after it was answered. This was the content before they edited it:


Hi,

I am trying to the plot the grid plot using the ggplot2 library, however, I am getting the error as given below. Please assist me with this.

> dput(head(res.mods.group))
structure(list(none = c(0, 0, 0, 0, 0, 0), Pandemic.influenza..A.H1N1.new.subtype. = c(-30.1204819277108, 
34.1935483870968, 41.7910447761194, -33.3333333333333, 17.0731707317073, 
0)), row.names = c("M16.14", "M16.2", "M16.26", "M15.73", "M15.21", 
"M14.72"), class = "data.frame")

> dput(head(Gen3_ann))
structure(list(Module = c("M4.1", "M5.1", "M6.2", "M7.3", "M8.1", 
"M9.9"), Cluster = c("A29", "A29", "A34", "A28", "A2", "A37"), 
    Cluster_location = c(1L, 4L, 4L, 6L, 1L, 1L), Function_New = c("Bio", 
    "TBD", "Cell", "Pathogenesis", "Toxicity", 
    "Erythrocytes"), position = c("A29.1", "A29.4", "A34.4", 
    "A28.6", "A2.1", "A37.1")), row.names = c("M4.1", "M5.1", "M6.2", "M7.3", "M8.1", 
"M9.9"), class = "data.frame")

library(reshape2)
library(ggplot2)

# Set parameters
GSE_ID = "GSE21802"
platform = "GPL6102"


## prepared cluter position
Group_plot = res.mods.group
Group_plot <-Group_plot[rownames(Gen3_ann),]
rownames(Group_plot)==rownames(Gen3_ann)                         # check if rownames is the same 
rownames(Group_plot) <- Gen3_ann$position
Group_plot <- as.data.frame(Group_plot)

head(Group_plot)

# creat new grid with all filtered cluster##
mod.group1 <- matrix(nrow=38,ncol=42)       
rownames (mod.group1) <- paste0("A",c(1:38))
colnames (mod.group1) <- paste0("",c(1:42))
##

virus_strain = colnames(Group_plot)
N.virus_strain = length(virus_strain)

i=1
for (i in 1:N.virus_strain){
  virus_strain = virus_strain[i]
  for (i in 1 : nrow(Group_plot)){
    Mx <- as.numeric(gsub(x = strsplit (rownames(Group_plot)[i],"\\.")[[1]][[1]],pattern = "A",replacement = ""))
    My <- as.numeric(strsplit (rownames(Group_plot)[i],"\\.")[[1]][[2]])
    mod.group1[Mx,My] <- Group_plot[,virus_strain][i] 
  }
  mod.group <- mod.group1[-c(9:14,19:23),]
  melt_test <- melt(mod.group,id.var=c("row.names"))
  colnames(melt_test) = c("Aggregate","Sub_aggregate","%Response")
  pdf(paste0(GSE_ID, "_", platform, "_Group_comparison_to_control", virus_strain, "_Grid.pdf"), height = 5.5, width = 8.5)
  plot = ggplot(melt_test, aes(Aggregate, as.factor(Sub_aggregate))) +
    geom_tile(color="#E6E6E6" , size = 0.2, fill=color )+
    geom_point(aes(colour=`%Response`),size=4.5)+ 
    ylab("") +
    xlab("") +
    labs(title= "Pandemic Infleunza vs Control")+
    theme(axis.text.x = element_text(angle = -90, hjust = 0))+
    scale_color_gradient2(low = "blue", mid="white", high = "red",limits=c(-100,100), na.value = "#E6E6E6", guide = "colourbar")+
    theme_light() +
    theme(panel.grid.minor = element_line(colour="black", size=0.9))+
    coord_flip() + 
    scale_x_discrete(limits = rev(levels(melt_test$Aggregate))) +
    theme(panel.border = element_rect(color = "black",size = 0.5),
          axis.text.x = element_text(colour="black",size=9,angle=0,hjust=0.5,vjust=2,face="plain"),
          axis.text.y = element_text(colour="black",size=9,angle=0,hjust=0.5,vjust=0.5,face="plain"))

  plot(plot)
  dev.off()
}

Error in `[.data.frame`(Group_plot, , virus_strain) : 
  undefined columns selected

Thank you,

Toufiq


ggplot2 data.frame grid plot geom_point • 462 views
ADD COMMENT
0
Entering edit mode

The error message indicates that one (or more) iterations of virus_strain lead to values that are not actually found in Group_plot.

I would wager that this line is the problem:

virus_strain = virus_strain[i]

You're overwriting virus_strain in the first iteration with virus_strain[i].

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0
Entering edit mode

Hi @Friederike,

Thank you very much for looking into this.

So, should I remove this code?

virus_strain = virus_strain[i]
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3
Entering edit mode
19 months ago
Carambakaracho ★ 2.8k

no, then your code won't work any more, as you reference virus_strain two more times. Rename the single element and all occurrences to something like this_strain

this_strain = virus_strain[i]
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0
Entering edit mode

Hi @ Carambakaracho,

Thank you, this is resolved.

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3
Entering edit mode

Hi, it looks like you changed your question after it was resolved. Please do not do that - it is extremely bad etiquette.You can add content if you absolutely need to, but do not remove content - the whole post loses meaning if you do that.

I have restored the content that was previously there. Fortunately, Google cache had a copy of it. If not, this would not have been possible.

Also, if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Upvote|Bookmark|Accept

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0
Entering edit mode

Hi @RamRS ,

Apologies. I had two browser tabs opened, most likely I might have deleted content from one tab.

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