Unsure about the mantel test result

[B-1991-ing]

Hi Houyun,

I carefully looked into the changing trend of my two matrixes, and not sure my command lines were right. So, could you please help me have a check? I attached my data and code.

data_and_code.zip

Thank you very much.

Best,

Bing

[Hy4m]

I had no problems after the test, and can you tell me what your problem is?

library(linkET)
library(dplyr)
library(ggplot2)
data_o <- read.table(file.choose(), sep="\t", row.names = 1, header = TRUE)

O_e <- read.table(file.choose(), sep="\t", row.names = 1, header = TRUE)


###mantel test
mantel_oms <- mantel_test(data_o, O_e,  
                          spec_select = list(m1 = 1:1, 
                                             m2 = 2:2, 
                                             m3 = 3:3, 
                                             m4 = 4:4,
                                             m5 = 5:5,
                                             m6 = 6:6,
                                             m7 = 7:7,
                                             m8 = 8:8),
                          spec_dist = dist_func(.FUN = "vegdist",
                                                method = "euclidean")) %>% 
  mutate(rd = cut(r, breaks = c(-Inf, 0.2, 0.4, Inf),
                  labels = c("< 0.2", "0.2 - 0.4", ">= 0.4")),
         pd = cut(p, breaks = c(-Inf, 0.01, 0.05, Inf),
                  labels = c("< 0.01", "0.01 - 0.05", ">= 0.05")))

o_plot <- correlate(O_e, engine = "correlation") %>% 
  as_md_tbl(type = "lower", diag = FALSE) %>%
  qcorrplot() +
  geom_square() +
  geom_mark(
    sep = '\n', 
    size = 3,
    sig_level = c(0.05, 0.01, 0.001),
    mark = c("*", "**", "***"),
    colour = "#000000", only_mark = FALSE) +
  
  scale_fill_gradientn(
    colours = colorRampPalette(colors =c("#A6CEE3","white","#ED665D"),space="Lab")(10),
    limits = c(-1, 1),
    breaks = seq(-1,1,0.5))+ 
  
  geom_couple(aes(x = .x - 0.2, colour = pd, size = rd, linetype = r > 0),
              
              data = mantel_oms, 
              curvature = nice_curvature(0.1), label.size =4, nudge_x= 0.2) + 
  
  scale_size_manual(values = c(0.5, 1, 2)) +
  
  scale_color_manual(values = c("#d00000", "#fcbf49","#d9d9d9")) +  
  #scale_color_manual(values = c("#d9d9d9")) +  
  scale_linetype_manual(values = c("TRUE" = "solid", "FALSE" = "dashed"),
                        labels = c("Positive", "Negative")) +
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1, vjust = 1)) +
  
  guides(size = guide_legend(title = "Mantel's r",
                             override.aes = list(colour = "grey35"), 
                             order = 2),
         colour = guide_legend(title = "Mantel's p", 
                               override.aes = list(size = 3), 
                               order = 1),
         fill = guide_colorbar(title = "Pearson's r", order = 4),
         linetype = guide_legend(title = "Mantel's r > 0", 
                                 override.aes = list(size = 0.5, colour = "darkblue"), 
                                 order = 3))
o_plot

[B-1991-ing]

Thank you Houyun.

My problem is that all significant relationships are denoted as positive relationship instead of some significant positive relationship and some significant negative relationship. I know I asked once. Sorry for the double asking. Maybe you can close the question.

Best,

Bing

[Hy4m]

I think it's OK.

Finally, it's better to email me for similar questions rather than an issue, since it's not a question about linkET package.