hy4m / linket Goto Github PK

Hi,

Thank you for this great package!

I use your code example (linkET v.0.07.1) below:

mantel_test(varespec, varechem,
spec_select = list(spec01 = 1:5, spec02 = 6:12))
'mantel_test()' using 'bray' dist method for 'spec'.
'mantel_test()' using 'euclidean' dist method for 'env'.

which applies bray to spec.

However, on my 16S amplicon dataset, I would like to manually specify the distance for spec and chem becaue by default it always applies euclidean distances to my species data but I want to use Bray-Curtis.

In the help manual to mantel_test(), I found that you can specify spec_dist = and env_dist =, however, the function dist_func() does not seem to offer the usually applied distances found in e.g. vegan::vegdist(method = "bray").

Could you please provide an example of how to specify e.g. Bray-Curtis using dist_func().
Also when looking up the help page for dist_func() one gets redirected to gdist(), without a clear explanation of how they relate and are supposed to be implemented in the mantel_test().

Thank you for helping and for sharing your expertise!

library(linkET)
as_matrix_data(mtcars, cluster = "all")
#> Error in attr(x, i) <- attrs[[i]]: cannot set attribute on a symbol

^{Created on 2021-09-26 by the reprex package (v2.0.0)}

您好，我在绘制mantel test相关性热图的时候没有展示对角线上的相关性数据，但是这让我的相关性热图的方块都很小。我的相关性热图的相关性系数范围时-0.2到0.2（排除了对角线上的相关系数），现在我想将geom_square的范围调到-0.2到0.2之间，我应该怎么做呢？

Hi Houyun,

How do you usually do when your matrix have some missed values? If I don't fill the missed values, I will have error when using the linkET.

Matrix
matrix.txt

Thank you very much.

Best,

Bing

为什么demo的数据可以跑出图，但是用自己的数据会出现这个问题

Hi Houyun,

When I try to load the linkET package --- library(linkET) today, error shown as below.
Error
namespace ‘vctrs’ 0.5.1 is already loaded, but >= 0.5.2 is required

I tried to reinstall the linkET package and the vctrs package, but failed.
install.packages("devtools")
devtools::install_github("Hy4m/linkET", force = TRUE)
install.packages("vctrs")

What can I do for this problem?

Best,

Bing

从Github安装失败：错误: Failed to install 'linkET' from GitHub:
Multiple results for CFLAGS found, something is wrong.FALSE
以下是我的版本信息：
_
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 2.3
year 2023
month 03
day 15
svn rev 83980
language R
version.string R version 4.2.3 (2023-03-15)
nickname Shortstop Beagle

我从您的GitHub库也没找到tar.gz源文件，请问您这怎么解决？

先感谢非常好用的包
出图的结果希望，热图部分能进行聚类再展示，可以实现吗

library(linkET)
correlate(mtcars) %>% 
  qcorrplot(extra_mat = list(extra = matrix(1, nrow = 11, ncol = 11))) +
  geom_square()
#> Error in as_md_tbl(data, ...): 参数没有用(extra_mat = list(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)))

^{Created on 2021-09-23 by the reprex package (v2.0.0)}

Hi Houyun,

Could you add one feature requirement to show the negative correlation using the dotted curves and the positive correlation using the solid curves? Then it will be easier for people to directly see the negative or positive correlation between two matrixes.

For now, all my correlated curves are solid.

Best,

Bing

Hi Houyun,

I want to see the correlation between two dataframe using linkET, but one dataframe has missing values - NA.

Should I move out the rows with NA? Or replace the NA using 0?
What I am doing now is to replace the NA with 0, but not sure if it is right.

Could you give me some suggestions?

Best,

Bing

Hello, I would like to inquire if the linkET package can run a data volume of over 20000 lines?

Hi, can I set the dote(spec data) in my own order?

When i use the example for qcorrplot
correlate(mtcars) %>% as_md_tbl() %>% qcorrplot()
it's return :
Error: Need a cor_tbl.

I found a R package named correlation with many different kinds of correlations. So would you like to intergrate it into linkET?

library(linkET)
data("varespec", package = "vegan")
data("varechem", package = "vegan")
random_forest(varespec[1:3], varechem[1:3])
#> Error:  'rp.importance' is not an exported object from 'namespace:rfPermute'

^{Created on 2021-10-11 by the reprex package (v2.0.1)}

不太清楚现在是否可以实现改变Mantel test连线起点和终点的形状和颜色？如果可以实现的话，使用哪个函数呢？

I want give bray curtis distance in spec_dist and euclidean distance in env_dist but unfortunately I unable to give and it automatically taking euclidean distance for both the data. How to set different distance matrix for both the data in matel_test() function.

Hi Houyun,

I am using the linkET to see the correlation between two matrixes, error always happened in the Rstudio.

Error screenshot

The code
linkET_Sib_amo_cox_code.pdf

The excel table
omstrup33_sillebotten_mam copy.xlsx

Do you have any idea why it always occcurs?

Best,

Bing

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

as the title, and i had tried several ways to achieve this.

• scale_x_discrete: not in avail. And there are glaring wrong with the square.
• ggtext::markdown: not in avail.
• linkET::element_formula: with parse=T, there is nothing change with the orgin label, that is, remain displaying CO[2] on the figure.
• linkET::latex_formula: not in avail. this function change CO[2] to CO *'['*, 2, *']'* and then just straightfoward display in the figure.

here's the figure with problem, and code attach it. Figure is the result when try the function ggtext::element_markdown and scale_x_discrete as description above.

qcorrplot(correlate(na.omit(eda.lon[,3:9])), type = "lower", diag = F)+
  geom_square() +
  # geom_tile()+
  scale_x_discrete(labels = eda.abbr)+
  scale_y_discrete(labels = eda.abbr)
  geom_couple(aes(colour = pd, size = rd), 
              data = mantel.mod, 
              curvature = nice_curvature()) +
  # geom_mark(r = NA,size = 3,only_mark = T)+
  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(11, "RdBu"),breaks = seq(1, -1, -0.4),limits = c(-1,1)) +
  scale_size_manual(values = c(0.5, 1, 2)) +
  scale_colour_manual(values = color_pal(3)) +
  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 = 3))+
  theme(
    axis.text = element_markdown(color = "black",size = 10))