one stack is missing in stacked barplot (ggplot2)

[shamimashrafiyan]

I have 5 methods and I would like to have a stack bar for each of them in a way that each bar has three stacks that each stack shows a range of values. fail: values less that 0.3, intermediate: values between 0.3 and 0.7, and high: values are more thatn 0.7
I have specific colors for methods and specific patterns for stacks. this is output of my code.

as you can see, "fail" stack is missing although I have fail vin my dataframe. also like to mention that for some values I had NAs in value column that I replaced with 0.
melted_df has four columns, named: Name, methods, values, stack_level

this is my code:

library(dplyr)
library(ggplot2)
library(reshape2)
library(ggpattern)

melted_df <- melt(AA, id.vars = "Name", variable.name = "method")
 melted_df$value[is.na(melted_df$value)] <- 0
 melted_df$value[(melted_df$value) < = 0] <- 0

breaks <- c(0, 0.3, 0.7, 1)
# Function to assign stack level based on value
assign_stack <- function(value) {
  if (value <= 0.3 && value >= 0) {
    return("fail")
  } else if (0.3 < value  && value < 0.7) {
    return("intermediate")
  } else if (value >= 0.7){
    return("high")
  }
}

# Apply the function to create a new column for stacking
melted_df$stack_level <- sapply(melted_df$value, assign_stack)
melted_df$stack_level <- factor(melted_df$stack_level, levels = c("high", "intermediate", "fail"))
Final_plot <- ggplot(melted_df, aes(x = method, y = value, fill = method)) +
  geom_col_pattern(aes(fill=method, pattern=stack_level, pattern_type = stack_level)
                   # ,colour='red'
                   ,pattern_density = 0.15
                   ,pattern_colour = "white"
                   ,pattern_fill = "white"
  ) + 
  
  labs(title = "Stacked Barplot with Value Ranges") + 
  geom_bar(stat = "identity",position = "dodge") +
  scale_fill_manual(values = c(gRF_Cor_test = "#33BBEE",STITCHIT_cor = "#b0b0b0",NN_Cor_test = "#083954",ugRF_test_cor = "#fae039", CNN_test_cor = "#ab0303"))+
  scale_pattern_manual(values=c(high = "circle",intermediate =  "stripe",fail = "none")) +
  scale_pattern_type_manual(values=c(NA, NA,NA ))+
  scale_pattern_fill_viridis_d() +
  theme_bw() +
  labs(x = "Method", title = "Stacked Barplot with Value Ranges") 
ggsave("/path/", plot = Final_plot, device = "pdf")

does anyone know what the problem is?
thanks in advance

[dromano]

It looks to me like the fail bars are there, but are very short. What happens if you run the following?:

melted_df |> 
  count(stack_level, method)

[shamimashrafiyan]

@dromano thanks for your reply, Actually Im getting this error
Error in FUN(X[[i]], ...) : object 'high' not found

but these are number of different stacks:
high:782
fail: 216
intermediate: 1106

BTW, I also ran the code for a bigger dataset that it has same number of gene for every method (it means, height of all 5 bars should be same), again bars just have two stacks and different height, thats why Im sure the fail part is missing.

[dromano]

Could you run the statement dput(AA) and paste the result here, like this?

``` r
<-- place output here
```

[shamimashrafiyan]

I think I found where this error comes from, but I dont know how to fix it.

ggplot(melted_df, aes(x = method, y = value, fill = method)) +

in the above line Im assigning value to y. I got stack_level based on my value but I should assign count of my stack levels to y. I mean (number of fail, intermediate and high), then the plot works properly. but how can I do that?

I need to mention that fail is not missing but its really small which is wrong, because the bars should have same height.

[shamimashrafiyan]

structure(list(gene = c("ENSG00000000003", "ENSG00000000005", 
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0.767251603837606)), row.names = c(NA, 100L), class = "data.frame")

this is first 100 rows of the AA.

[dromano]

Thanks, though this is a different table from the one you used in the code for your original post — the melt() command fails on it because the column names are different. Could you share the original so that the code works?