VolcanoPlot error with x_cutoff

[tonypanx]

I get this error when I set x_cutoff to any value other than 0:

Error in scale$guide == "none" : comparison (1) is possible only for atomic and list types

[pwwang]

Is this related to #8 ?

[tonypanx]

#8 refers to the xlim, this issue refers to the x_cutoff line. I clarify what I mean in the other issue.

[pwwang]

Can you post a minimal and runnable code to reproduce?

[tonypanx]

VolcanoPlot(markers, x = 'avg_log2FC', y = 'p_val_adj', x_cutoff = 1, label_size = 4, flip_negatives = F, y_cutoff = 10^-2, highlight_color = 'orange', pt_alpha = 0.8)

[pwwang]

Again, I can't reproduce it with the data from builtin examples:

set.seed(8525)
# Obtained by Seurat::FindMakers for the first cluster of pbmc_small
data <- data.frame(
   avg_log2FC = c(
     -3.69, -4.10, -2.68, -3.51, -3.09, -2.52, -3.53, -3.35, -2.82, -2.71, -3.16, -2.24,
     -5.62, -3.10, -3.42, -2.72, -3.23, -3.25, -4.68, 3.67, -2.66, 4.79, -2.99, 10.14,
     -1.78, -2.67, -2.26, -2.59, -3.39, 5.36, 4.56, 4.62, -2.94, -9.47, -9.12, -1.63,
     -2.77, 3.31, -1.53, -3.89, -4.21, 4.72, -2.98, -2.29, -1.41, -9.48, -4.30, 3.01,
     -1.19, -4.83, -1.35, -1.68, -1.63, -2.70, 3.86, 3.81, 7.23, -1.45, -0.92, -2.45,
     3.91, -4.45, -9.33, 3.56, 2.27, -1.60, -1.15, 11.40, -9.77, -8.32, 2.61, -1.25,
     -1.72, 10.61, 11.34, 10.02, 2.78, -3.48, -1.98, 5.86, 5.57, 4.57, 9.75, 9.97,
     10.90, 9.19, 2.93, 5.10, -1.52, -3.93, -1.95, -2.46, -0.64, 4.60, -1.82, -0.80,
     9.34, 7.51, 6.45, 5.23, 4.41, 3.60, -1.94, -1.15),
   p_val_adj = c(
     3.82e-09, 1.52e-07, 1.79e-07, 4.68e-07, 4.83e-07, 6.26e-07, 2.61e-06, 1.33e-05,
     1.79e-05, 3.71e-05, 5.21e-05, 5.36e-05, 5.83e-05, 6.66e-05, 8.22e-05, 2.89e-04,
     3.00e-04, 4.94e-04, 7.62e-04, 8.93e-04, 9.55e-04, 9.61e-04, 1.12e-03, 1.47e-03,
     1.66e-03, 1.95e-03, 2.06e-03, 3.01e-03, 3.26e-03, 4.35e-03, 4.85e-03, 5.12e-03,
     5.40e-03, 7.18e-03, 7.18e-03, 1.04e-02, 1.24e-02, 1.90e-02, 1.94e-02, 1.97e-02,
     2.09e-02, 2.13e-02, 2.25e-02, 2.61e-02, 3.18e-02, 3.27e-02, 3.69e-02, 3.80e-02,
     4.95e-02, 5.73e-02, 5.77e-02, 6.10e-02, 6.22e-02, 6.31e-02, 6.72e-02, 9.23e-02,
     9.85e-02, 1.06e-01, 1.07e-01, 1.11e-01, 1.31e-01, 1.38e-01, 1.40e-01, 1.43e-01,
     2.00e-01, 2.39e-01, 2.49e-01, 2.57e-01, 2.86e-01, 2.86e-01, 2.98e-01, 3.32e-01,
     4.15e-01, 4.91e-01, 4.91e-01, 4.91e-01, 5.97e-01, 7.11e-01, 7.59e-01, 8.38e-01,
     9.20e-01, 9.20e-01, 9.29e-01, 9.29e-01, 9.29e-01, 9.29e-01, 9.34e-01, 9.68e-01,
     1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00,
     1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00, 1.00e+00),
   gene = c(
     "HLA-DPB1", "LYZ", "HLA-DRA", "TYMP", "HLA-DPA1", "HLA-DRB1", "CST3", "HLA-DQB1",
     "HLA-DRB5", "LST1", "HLA-DQA1", "AIF1", "S100A8", "IFITM3", "HLA-DMB", "FCGRT",
     "SERPINA1", "IFI30", "S100A9", "CCL5", "GRN", "LCK", "HLA-DMA", "MS4A6A", "CTSS",
     "CFP", "FCN1", "BID", "CFD", "CD3D", "CD7", "CD3E", "LGALS2", "CD14", "SMCO4",
     "LINC00936", "HCK", "CTSW", "LGALS1", "HLA-DQA2", "LRRC25", "GZMM", "RNF130",
     "LGALS3", "S100A11", "C5AR1", "IL1B", "GZMA", "FCER1G", "MPEG1", "TYROBP", "TSPO",
     "GSTP1", "CTSB", "IL32", "CD247", "GNLY", "COTL1", "NFKBIA", "NUP214", "LAMP1",
     "FPR1", "CLEC10A", "CST7", "PRF1", "BLVRA", "PSAP", "GZMH", "EAF2", "ASGR1",
     "RARRES3", "SAT1", "LY86", "GP9", "TUBB1", "NGFRAP1", "XBP1", "SCO2", "RGS2", "GZMB",
     "HIST1H2AC", "KLRD1", "PGRMC1", "AKR1C3", "PTGDR", "IL2RB", "GYPC", "CCL4", "CD68",
     "FCER1A", "CD79B", "MS4A7", "CARD16", "ACAP1", "CD79A", "ANXA2", "TMEM40", "PF4",
     "GNG11", "CLU", "CD9", "FGFBP2", "TNFRSF1B", "IFI6"),
  pct_diff = c(
     -0.752, -0.457, -0.460, -0.671, -0.626, -0.701, -0.502, -0.619, -0.623, -0.598,
     -0.566, -0.626, -0.543, -0.566, -0.541, -0.542, -0.515, -0.489, -0.444, 0.428,
     -0.517, 0.461, -0.491, -0.410, -0.480, -0.491, -0.521, -0.491, -0.438, 0.411,
     0.411, 0.409, -0.438, -0.359, -0.359, -0.440, -0.386, 0.385, -0.332, -0.361, -0.361,
     0.364, -0.387, -0.415, -0.454, -0.308, -0.335, 0.364, -0.454, -0.309, -0.379, -0.427,
     -0.377, -0.389, 0.335, 0.315, 0.313, -0.284, -0.502, -0.309, 0.313, -0.284, -0.256,
     0.309, 0.313, -0.364, -0.406, 0.244, -0.231, -0.231, 0.281, -0.311, -0.312, 0.220,
     0.220, 0.220, 0.261, -0.232, -0.367, 0.240, 0.218, 0.218, 0.195, 0.195, 0.195, 0.195,
     0.262, 0.218, -0.288, -0.207, -0.290, -0.233, -0.367, 0.217, -0.233, -0.403, 0.171,
     0.194, 0.194, 0.194, 0.194, 0.213, -0.235, -0.292),
  group = sample(LETTERS[1:2], 104, replace = TRUE)
)
rownames(data) <- data$gene

VolcanoPlot(data, x = 'avg_log2FC', y = 'p_val_adj', x_cutoff = 1, label_size = 4,
    flip_negatives = F,  y_cutoff = 10^-2, highlight_color = 'orange', pt_alpha = 0.8)

[tonypanx]

I tried to reproduce the example with the code provided but obtained the same error:

Error in scale$guide == "none" : comparison (1) is possible only for atomic and list types

Here is the error traceback and my session info:

12: isTRUE(scale$guide == "none")
11: FUN(X[[i]], ...)
10: lapply(scales, bump_aes_scale, new_aes = new_aes)
9: bump_aes_scales(plot$scales$scales, new_aes = object)
8: ggplot_add.new_aes(object, p, objectname)
7: ggplot_add(object, p, objectname)
6: add_ggplot(e1, e2, e2name)
5: +.gg(p, new_scale_color())
4: VolcanoPlotAtomic(datas[[nm]], x = x, y = y, ytrans = ytrans,
color_by = color_by, color_name = color_name, flip_negatives = flip_negatives,
x_cutoff = x_cutoff, y_cutoff = y_cutoff, x_cutoff_name = x_cutoff_name,
y_cutoff_name = y_cutoff_name, x_cutoff_color = x_cutoff_color,
y_cutoff_color = y_cutoff_color, x_cutoff_linetype = x_cutoff_linetype,
y_cutoff_linetype = y_cutoff_linetype, x_cutoff_linewidth = x_cutoff_linewidth,
y_cutoff_linewidth = y_cutoff_linewidth, pt_size = pt_size,
pt_alpha = pt_alpha, nlabel = nlabel, labels = labels, label_size = label_size,
label_fg = label_fg, label_bg = label_bg, label_bg_r = label_bg_r,
highlight = highlight, highlight_color = highlight_color,
highlight_size = highlight_size, highlight_alpha = highlight_alpha,
highlight_stroke = highlight_stroke, facet_by = facet_by,
facet_scales = facet_scales, facet_ncol = facet_ncol, facet_nrow = facet_nrow,
facet_byrow = facet_byrow, theme = theme, theme_args = theme_args,
palette = palette, palcolor = palcolor, title = title, subtitle = subtitle,
xlab = xlab, ylab = ylab, aspect.ratio = aspect.ratio, legend.position = legend.position,
legend.direction = legend.direction, seed = seed, ...)
3: FUN(X[[i]], ...)
2: lapply(names(datas), function(nm) {
default_title <- if (length(datas) == 1 && identical(nm,
"..."))
NULL
else nm
if (is.function(title)) {
title <- title(default_title)
}
else {
title <- title %||% default_title
}
VolcanoPlotAtomic(datas[[nm]], x = x, y = y, ytrans = ytrans,
color_by = color_by, color_name = color_name, flip_negatives = flip_negatives,
x_cutoff = x_cutoff, y_cutoff = y_cutoff, x_cutoff_name = x_cutoff_name,
y_cutoff_name = y_cutoff_name, x_cutoff_color = x_cutoff_color,
y_cutoff_color = y_cutoff_color, x_cutoff_linetype = x_cutoff_linetype,
y_cutoff_linetype = y_cutoff_linetype, x_cutoff_linewidth = x_cutoff_linewidth,
y_cutoff_linewidth = y_cutoff_linewidth, pt_size = pt_size,
pt_alpha = pt_alpha, nlabel = nlabel, labels = labels,
label_size = label_size, label_fg = label_fg, label_bg = label_bg,
label_bg_r = label_bg_r, highlight = highlight, highlight_color = highlight_color,
highlight_size = highlight_size, highlight_alpha = highlight_alpha,
highlight_stroke = highlight_stroke, facet_by = facet_by,
facet_scales = facet_scales, facet_ncol = facet_ncol,
facet_nrow = facet_nrow, facet_byrow = facet_byrow, theme = theme,
theme_args = theme_args, palette = palette, palcolor = palcolor,
title = title, subtitle = subtitle, xlab = xlab, ylab = ylab,
aspect.ratio = aspect.ratio, legend.position = legend.position,
legend.direction = legend.direction, seed = seed, ...)
})
1: VolcanoPlot(data, x = "avg_log2FC", y = "p_val_adj", x_cutoff = 1,
label_size = 4, flip_negatives = F, y_cutoff = 10^-2, highlight_color = "orange",
pt_alpha = 0.8)

version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el8-x86_64/lib/libopenblas_skylakexp-r0.3.13.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] scplotter_0.0.2 dplyr_1.1.4 plyr_1.8.9

loaded via a namespace (and not attached):
[1] tinytex_0.38 circlize_0.4.15 shape_1.4.6 spam_2.8-0 zoo_1.8-11 tidyselect_1.2.0 xfun_0.38
[8] purrr_1.0.1 listenv_0.8.0 lattice_0.20-45 colorspace_2.0-3 vctrs_0.6.5 generics_0.1.3 utf8_1.2.2
[15] rlang_1.1.4 gridtext_0.1.5 pillar_1.9.0 glue_1.6.2 sp_1.6-0 lifecycle_1.0.4 stringr_1.5.1
[22] dotCall64_1.0-1 munsell_0.5.0 gtable_0.3.0 progressr_0.10.0 future_1.25.0 GlobalOptions_0.1.2 codetools_0.2-18
[29] forcats_1.0.0 parallel_4.2.0 fansi_1.0.3 Rcpp_1.0.13 scales_1.3.0 showtext_0.9-7 plotthis_0.5.0
[36] sysfonts_0.8.9 parallelly_1.31.1 ggplot2_3.5.1 digest_0.6.29 stringi_1.8.3 showtextdb_3.0 ggrepel_0.9.3
[43] SeuratObject_5.0.1 grid_4.2.0 cowplot_1.1.1 cli_3.6.2 tools_4.2.0 magrittr_2.0.3 patchwork_1.2.0
[50] tibble_3.2.1 tidyr_1.3.0 future.apply_1.9.0 pkgconfig_2.0.3 Matrix_1.6-4 ggnewscale_0.4.8 xml2_1.3.3
[57] rstudioapi_0.14 R6_2.5.1 globals_0.14.0 ggtext_0.1.2 compiler_4.2.0

[pwwang]

scplotter_0.0.2 is way outdated. Try the latest version.

[tonypanx]

I updated to scplotter 0.2.0, same issue.

[pwwang]

Maybe try to upgrade ggnewscale to 0.5.0.

I saw similar issues reported here.

[tonypanx]

The update solved the issue, thanks!