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PhanstielLab / plotgardener

https://phanstiellab.github.io/plotgardener/
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'argument "chrom" is missing, with no default' when using axis="y" for annoGenomeLabel #87

Closed chualec closed 1 year ago

chualec commented 1 year ago

Hi, I've been trying to use the plot genome y axis function, but it doesn't really work for me It gives me this error: argument "chrom" is missing, with no default

Please let me know if there is something wrong with how i am interpreting the code. Thanks.

This is the code i used:

gene_A.chrom <- "chr3" gene_A.start <- 127686231 gene_A.end <- 127792951 gene_B.chrom <- "chr3" gene_B.start <- 127686231 gene_B.end <- 127792951

pageCreate(width = 10, height = 5, default.units = "inches") test <- expand.grid(chr8=round(seq(gene_A.start, gene_A.end, 10000), -4), chr3=round(seq(gene_B.start, gene_B.end, 10000), -4)) test <- test %>% relocate(chr3) test$counts <- rnorm(nrow(test), mean=100, sd=50)

params_a <- pgParams(chrom=gene_A.chrom, chromstart = gene_A.start, chromend = gene_A.end, altchrom = gene_B.chrom, altchromstart = gene_B.start, altchromend = gene_B.end, resolution = 10000, assembly = "hg38", x = 3.25, width = 2.75, just = c("left", "top"), default.units = "inches")

hicPlot_top <- plotHicSquare(data = test, params = params_a, zrange = c(0, 1), resolution = 10000, half = "top", y = 0.5, height = 2.75, draw=T) hicPlot_bottom <- plotHicSquare(data = test, params = params_a, zrange = c(0, 1), resolution = 10000, half = "bottom", y = 0.5, height = 2.75, draw=T)

genes_a <- plotGenes(params = params_a, stroke = 1, fontsize = 6, y = 3.35, height = 0.4)

annoGenomeLabel(plot = genes_a, params = params_a, scale = "Mb", fontsize = 7, y = 3.85)

annoGenomeLabel(plot = genes_a, params = params_a, scale = "Mb", fontsize = 7, y = 3.85, axis="y")

pageGuideHide()

nekramer commented 1 year ago

Hi there! This error is occurring due to the plot type specified in your annoGenomeLabel call. Y-axis genome labels only work for plots that have a genomic axis along the y-axis, which is currently only possible with plotHicSquare. Even though you've specified altchrom in the params object, plotGenes does not parse this because it can only handle chrom. Thus, when you call a y-axis annoGenomeLabel with the genes plot object, it cannot find an altchrom to parse and assumes the chromosome is NULL, throwing that error. However, if you passed your square Hi-C plot into this call, it would be able to find that altchrom and create the genome label.

Best, Nicole

chualec commented 1 year ago

Hi Nicole,

Thanks! using "annoGenomeLabel(plot = hicPlot_top, params = params_a, scale = "Mb", fontsize = 7, y = 3.85, axis="y")" successfully solve the problem.

Thanks!