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Showing content from https://github.com/jafarilab/NIMAA/tree/v0.1.0 below:

GitHub - jafarilab/NIMAA at v0.1.0

The goal of NIMAA is to use bipartite graphs for nominal data mining.

It can select a larger sub-matrix with no missing values in a matrix containing missing data, and then use the matrix to generate a bipartite graph and cluster on two projections. In addition, NIMAA can also impute the missing data, verify and score according to the previous clustering results obtained from the sub-matrix, and give suggestions on which imputation method is better.

You can install the released version of NIMAA from CRAN with:

install.packages("NIMAA")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("jafarilab/NIMAA")

library(NIMAA)
## load the beatAML data
beatAML_data <- NIMAA::beatAML

# plot the original data
beatAML_incidence_matrix <- plotInput(
  x = beatAML_data, # original data with 3 columns
  index_nominal = c(2,1), # the first two columns are nominal data
  index_numeric = 3,  # the third column inumeric data
  print_skim = FALSE, # if you want to check the skim output, set this as TRUE(Default)
  plot_weight = TRUE, # when plotting the figure, show the weights
  )
#> 
#> Na/missing values Proportion:     0.2603

beatAML dataset as incidence matrix

graph <- plotBipartite(inc_mat = beatAML_incidence_matrix)

extractSubMatrix() will extract the sub-matrices which have no missing value inside or with specific proportion of missing values inside (not for elements-max matrix), depends on the user’s input.

sub_matrices <- extractSubMatrix(
  beatAML_incidence_matrix,
  shape = c("Square", "Rectangular_element_max"), # the shapes you want to extract
  row.vars = "patient_id",
  col.vars = "inhibitor",
  plot_weight = T,
  )

Row-wise arrangement

Column-wise arrangement

findCluster() will perform optional pre-processing on the input incidence matrix, such as normalization. Then use the matrix to perform bipartite graph projection, and perform optional pre-processing in one of the specified parts, such as removing edges with lower weights, that is, weak edges.

cls <- findCluster(
  sub_matrices$Rectangular_element_max,
  dim = 1,
  method = "all", # clustering mehod
  normalization = TRUE, # normalize the input matrix
  rm_weak_edges = TRUE, # remove the weak edges in graph
  rm_method = 'delete', # removing method is deleting the edges
  threshold = 'median', # edges with weights under the median of all edges' weight are weak edges
  set_remaining_to_1 = TRUE, # set the weights of remaining edges to 1
  )

The imputeMissingValue() function can impute the missing values in the matrix, we only need to select which methods are needed. The result will be a list, each element is a matrix with no missing values.

it will perform a variety of numerical imputation according to the user’s input, and return all the data that does not contain any missing data, a list of matrices.

• ‘median’ will replace the missing values with the median of each rows (observations)

• ‘knn’ is the method in package

• ‘als’ and ‘svd’ are methods from package

• ‘CA’, ‘PCA’ and ‘FAMD’ are from package

• others are from the famous package.

imputations <- imputeMissingValue(
  inc_mat = beatAML_incidence_matrix,
  method = c('svd','median','als','CA')
  )

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