DiffPlot `<scale>` argument of `guides()`

[FlavianR]

Hi! Thanks for this great tool, as always!! I have an issue on the DiffPlot, when I try to use it a warning rise and the plot isn't generated. I wanted to save the plot in a pdf file, and I used exactly the same command as in the documentation. In the file, i just have an empty page. The warning is : or (in terminal) :

When I call lifecycle::last_lifecycle_warnings(), I obtain :

NB : I used ggplot2 3.4.2

[mdozmorov]

Hi @FlavianR, If I run the vignette and create a plot, I can plot it just fine.

# Running TADCompare as-is
TD_Compare <- TADCompare(mtx1, mtx2, resolution = res)
# Running the plotting algorithm with pre-specified TADs
p <- DiffPlot(tad_diff    = TD_Compare, 
              cont_mat1   = mtx1,
              cont_mat2   = mtx2,
              resolution  = res,
              start_coord = start_coord,
              end_coord   = end_coord,
              show_types  = TRUE, 
              point_size  = 5,
              max_height  = 5,
              rel_heights = c(1, 2),
              palette     = "RdYlBu")
plot(p)

To save it, we don't provide a specific code, but simple library(ggplot2); ggsave("demo.pdf") saves the plot.

In general, we recommend https://hicexplorer.readthedocs.io/en/latest/content/tools/hicPlotTADs.html for plotting.

[mdozmorov]

Please, let me know if you still have issues.

[FlavianR]

Hi! Sorry for the delay in responding! I try with your proposition but I still got the same issue. I think it's only a version problem when I try to use DiffPlot in script rather than in Rstudio (this 2 environments might defer). I will explore this and come back to you if I find a solution.

[mdozmorov]

If you could provide a reproducible example, that'll be great.

[FlavianR]

I can provide you a portion of my script but I can't provide my data, but for testing I used the test.mcool from Cooltools documentation. My matrices were generated using cooler dump and used in input of my Rscript. My code :

#Utilities 
library(TADCompare)
library(SpectralTAD)
library(dplyr)
library(data.table)

#Inputs 
if (length(args)<12) {
  stop("Need at least 5 inputs (-h/--help)", call.=FALSE)
}

input1 <- args[6]
input2 <- args[7]
res <- args[8]
chr <- args[9]
path_TAD_1 <- args[10]
path_TAD_2 <- args[11]
output <- args[12]
if (length(args)==14){
  start <- args[13]
  end <- args[14]
}

#PreProcess
print("Matrix 1")
mat1 <- fread(input1, data.table = FALSE)
print("Sparsing")
sparse_mat1 <- HiCcompare::cooler2sparse(mat1)
print("Spectral TAD")
Spec_1 <- SpectralTAD(sparse_mat1[[chr]], chr = chr, levels = 3)

print("Matrix 2")
mat2 <- fread(input2, data.table = FALSE)
print("Sparsing")
sparse_mat2 <- HiCcompare::cooler2sparse(mat2)
print("Spectral TAD")
Spec_2 <- SpectralTAD(sparse_mat2[[chr]], chr = chr, levels = 3)

list_TAD <- list(bind_rows(Spec_1), bind_rows(Spec_2))

# Process
print("TADCompare exe")
test <- TADCompare(sparse_mat1[[chr]], 
                   sparse_mat2[[chr]], 
                   resolution = as.numeric(res), 
                   pre_tads = list_TAD)

print("Graphique generation")
pdf(paste0(output,chr,"_AD_",res,".pdf"))
DiffPlot(tad_diff    = test, 
           cont_mat1   = sparse_mat1[[chr]],
           cont_mat2   = sparse_mat2[[chr]],
           resolution  = as.numeric(res),
           start_coord = as.numeric(start),
           end_coord   = as.numeric(end),
           pre_tad = list_TAD,
           show_types  = TRUE, 
           point_size  = 5,
           palette     = "RdYlBu",
           rel_heights = c(1, 2))
dev.off()

With this code TADCompare worked correctly, only DiffPlot have an issue.