## ----include = FALSE--------------------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
options(tibble.print_min = 4L, tibble.print_max = 4L)
options(width=90)
options(rmarkdown.html_vignette.check_title = FALSE)
set.seed(60)

## ----echo=FALSE-------------------------------------------------------------------------
spaces <- function (n) {
  paste(rep("&nbsp;", n), collapse = "")
}

## ----fig.align="right", echo=FALSE, out.width="25%", out.extra='style="float:right; padding:10px"'----
knitr::include_graphics(path = "../man/figures/Symbol.png", error = FALSE)

## ----setup------------------------------------------------------------------------------
library(influential)

## ----exptl_data_fcor, eval=FALSE--------------------------------------------------------
# 
# # Prepare a sample dataset
# set.seed(60)
# my_data <- matrix(data = runif(n = 10000, min = 2, max = 300),
#                        nrow = 50, ncol = 200,
#                        dimnames = list(c(paste("sample", c(1:50), sep = "_")),
#                                        c(paste("gene", c(1:200), sep = "_")))
# )

## ----fcor_calc, eval=FALSE--------------------------------------------------------------
# 
# # Calculate correlations between all pairs of genes
# 
# correlation_tbl <- fcor(data = my_data,
#                         method = "spearman",
#                         mutualRank = TRUE,
#                         pvalue = "TRUE", adjust = "BH",
#                         flat = TRUE)

## ----echo=FALSE-------------------------------------------------------------------------
knitr::kable(head(coexpression.data))

## ----g_dataframe------------------------------------------------------------------------
# Preparing the data
MyData <- coexpression.data

# Reconstructing the graph
My_graph <- graph_from_data_frame(d=MyData)

## ---------------------------------------------------------------------------------------
class(My_graph)

## ----echo=FALSE-------------------------------------------------------------------------
knitr::kable(head(coexpression.adjacency, n=15)[10:15,10:15])

## ----g_adj, eval=FALSE------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.adjacency
# 
# # Reconstructing the graph
# My_graph <- graph_from_adjacency_matrix(MyData)

## ----echo=FALSE-------------------------------------------------------------------------
set.seed(60)
My_Data <- matrix(data = sample(c(0,1), replace = TRUE, size = 20), 
                  nrow = 4, ncol = 5,
                  dimnames = list(c(paste("cell", c(1:4), sep = "_")),
                                  c(paste("Gene", c(1:5), sep = "_"))))

knitr::kable(My_Data)

## ----g_inc, eval=FALSE------------------------------------------------------------------
# # Reconstructing the graph
# My_graph <- graph_from_adjacency_matrix(MyData)

## ----g_sif, eval=FALSE------------------------------------------------------------------
# # Reconstructing the graph
# My_graph <- sif2igraph(Path = "Sample_SIF.sif")
# 
# class(My_graph)
# #> [1] "igraph"

## ----Vertices, eval=FALSE---------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# My_graph_vertices <- V(My_graph)
# 
# head(My_graph_vertices)
# #> + 6/794 vertices, named, from 775cff6:
# #> [1] ADAMTS9-AS2 C8orf34-AS1 CADM3-AS1   FAM83A-AS1  FENDRR      LANCL1-AS1

## ----DC, eval=FALSE---------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating degree centrality
# My_graph_degree <- degree(My_graph, v = GraphVertices, normalized = FALSE)
# 
# head(My_graph_degree)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>         172         121         168          26         189         176

## ----BC, eval=FALSE---------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating betweenness centrality
# My_graph_betweenness <- betweenness(My_graph, v = GraphVertices,
#                                     directed = FALSE, normalized = FALSE)
# 
# head(My_graph_betweenness)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>   21719.857   28185.199   26946.625    2940.467   33333.369   21830.511

## ----NC, eval=FALSE---------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating neighborhood connectivity
# neighrhood.co <- neighborhood.connectivity(graph = My_graph,
#                                            vertices = GraphVertices,
#                                            mode = "all")
# 
# head(neighrhood.co)
# #>  ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>   11.290698    4.983471    7.970238    3.000000   15.153439   13.465909

## ----H_index, eval=FALSE----------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating H-index
# h.index <- h_index(graph = My_graph,
#                    vertices = GraphVertices,
#                    mode = "all")
# 
# head(h.index)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>          11           9          11           2          12          12

## ----LH_index, eval=FALSE---------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating Local H-index
# lh.index <- lh_index(graph = My_graph,
#                    vertices = GraphVertices,
#                    mode = "all")
# 
# head(lh.index)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>        1165         446         994          34        1289        1265

## ----CI, eval=FALSE---------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating Collective Influence
# ci <- collective.influence(graph = My_graph,
#                           vertices = GraphVertices,
#                           mode = "all", d=3)
# 
# head(ci)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>        9918       70560       39078         675       10716        7350

## ----CR, eval=FALSE---------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculating ClusterRank
# cr <- clusterRank(graph = My_graph,
#                   vids = GraphVertices,
#                   directed = FALSE, loops = TRUE)
# 
# head(cr)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>   63.459812    5.185675   21.111776    1.280000  135.098278   81.255195

## ----cond.prob--------------------------------------------------------------------------
# Preparing the data
MyData <- centrality.measures        

# Assessing the conditional probability
My.conditional.prob <- cond.prob.analysis(data = MyData,       
                                          nodes.colname = rownames(MyData),
                                          Desired.colname = "BC",
                                          Condition.colname = "NC")

print(My.conditional.prob)

## ----double.cent.assess, eval=FALSE-----------------------------------------------------
# # Preparing the data
# MyData <- centrality.measures
# 
# # Association assessment
# My.metrics.assessment <- double.cent.assess(data = MyData,
#                                             nodes.colname = rownames(MyData),
#                                             dependent.colname = "BC",
#                                             independent.colname = "NC")
# 
# print(My.metrics.assessment)
# #> $Summary_statistics
# #>         BC NC
# #> Min.              0.000000000                   1.2000
# #> 1st Qu.           0.000000000                  66.0000
# #> Median            0.000000000                 156.0000
# #> Mean              0.005813357                 132.3443
# #> 3rd Qu.           0.000340000                 179.3214
# #> Max.              0.529464720                 192.0000
# #>
# #> $Normality_results
# #>                               p.value
# #> BC    1.415450e-50
# #> NC 9.411737e-30
# #>
# #> $Dependent_Normality
# #> [1] "Non-normally distributed"
# #>
# #> $Independent_Normality
# #> [1] "Non-normally distributed"
# #>
# #> $GAM_nonlinear.nonmonotonic.results
# #>      edf  p-value
# #> 8.992406 0.000000
# #>
# #> $Association_type
# #> [1] "nonlinear-nonmonotonic"
# #>
# #> $HoeffdingD_Statistic
# #>         D_statistic P_value
# #> Results  0.01770279   1e-08
# #>
# #> $Dependence_Significance
# #>                       Hoeffding
# #> Results Significantly dependent
# #>
# #> $NNS_dep_results
# #>         Correlation Dependence
# #> Results  -0.7948106  0.8647164
# #>
# #> $ConditionalProbability
# #> [1] 55.35386
# #>
# #> $ConditionalProbability_split.half.sample
# #> [1] 55.90331

## ----double.cent.assess.noRegr., eval=FALSE---------------------------------------------
# # Preparing the data
# MyData <- centrality.measures
# 
# # Association assessment
# My.metrics.assessment <- double.cent.assess.noRegression(data = MyData,
#                                                          nodes.colname = rownames(MyData),
#                                                          centrality1.colname = "BC",
#                                                          centrality2.colname = "NC")
# 
# print(My.metrics.assessment)
# #> $Summary_statistics
# #>         BC NC
# #> Min.              0.000000000                   1.2000
# #> 1st Qu.           0.000000000                  66.0000
# #> Median            0.000000000                 156.0000
# #> Mean              0.005813357                 132.3443
# #> 3rd Qu.           0.000340000                 179.3214
# #> Max.              0.529464720                 192.0000
# #>
# #> $Normality_results
# #>                               p.value
# #> BC    1.415450e-50
# #> NC 9.411737e-30
# #>
# #> $Centrality1_Normality
# #> [1] "Non-normally distributed"
# #>
# #> $Centrality2_Normality
# #> [1] "Non-normally distributed"
# #>
# #> $HoeffdingD_Statistic
# #>         D_statistic P_value
# #> Results  0.01770279   1e-08
# #>
# #> $Dependence_Significance
# #>                       Hoeffding
# #> Results Significantly dependent
# #>
# #> $NNS_dep_results
# #>         Correlation Dependence
# #> Results  -0.7948106  0.8647164
# #>
# #> $ConditionalProbability
# #> [1] 55.35386
# #>
# #> $ConditionalProbability_split.half.sample
# #> [1] 55.68163

## ----IVI.from.indices, eval=FALSE-------------------------------------------------------
# # Preparing the data
# MyData <- centrality.measures
# 
# # Calculation of IVI
# My.vertices.IVI <- ivi.from.indices(DC = MyData$DC,
#                                    CR = MyData$CR,
#                                    NC = MyData$NC,
#                                    LH_index = MyData$LH_index,
#                                    BC = MyData$BC,
#                                    CI = MyData$CI)
# 
# head(My.vertices.IVI)
# #> [1] 24.670056  8.344337 18.621049  1.017768 29.437028 33.512598

## ----IVI, eval=FALSE--------------------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculation of IVI
# My.vertices.IVI <- ivi(graph = My_graph, vertices = GraphVertices,
#                        weights = NULL, directed = FALSE, mode = "all",
#                        loops = TRUE, d = 3, scale = "range")
# 
# head(My.vertices.IVI)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>    39.53878    19.94999    38.20524     1.12371   100.00000    47.49356

## ----net.for.vis, eval=FALSE------------------------------------------------------------
# # Reconstructing the graph
# set.seed(70)
# My_graph <-  igraph::sample_gnm(n = 50, m = 120, directed = TRUE)
# 
# # Calculating the IVI values
# My_graph_IVI <- ivi(My_graph, directed = TRUE)
# 
# # Visualizing the graph based on IVI values
# My_graph_IVI_Vis <- cent_network.vis(graph = My_graph,
#                                      cent.metric = My_graph_IVI,
#                                      directed = TRUE,
#                                      plot.title = "IVI-based Network",
#                                      legend.title = "IVI value")
# 
# My_graph_IVI_Vis

## ----Spreading.score, eval=FALSE--------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculation of Spreading score
# Spreading.score <- spreading.score(graph = My_graph,
#                                    vertices = GraphVertices,
#                                    weights = NULL, directed = FALSE, mode = "all",
#                                    loops = TRUE, d = 3, scale = "range")
# 
# head(Spreading.score)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>   42.932497   38.094111   45.114648    1.587262  100.000000   49.193292

## ----Hubness.score, eval=FALSE----------------------------------------------------------
# # Preparing the data
# MyData <- coexpression.data
# 
# # Reconstructing the graph
# My_graph <- graph_from_data_frame(MyData)
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculation of Hubness score
# Hubness.score <- hubness.score(graph = My_graph,
#                                    vertices = GraphVertices,
#                                    directed = FALSE, mode = "all",
#                                    loops = TRUE, scale = "range")
# 
# head(Hubness.score)
# #> ADAMTS9-AS2 C8orf34-AS1   CADM3-AS1  FAM83A-AS1      FENDRR  LANCL1-AS1
# #>   84.299719   46.741660   77.441514    8.437142   92.870451   88.734131

## ----SIRIR, eval=FALSE------------------------------------------------------------------
# # Reconstructing the graph
# My_graph <-  sif2igraph(Path = "Sample_SIF.sif")
# 
# # Extracting the vertices
# GraphVertices <- V(My_graph)
# 
# # Calculation of influence rank
# Influence.Ranks <- sirir(graph = My_graph,
#                                    vertices = GraphVertices,
#                                    beta = 0.5, gamma = 1, no.sim = 10, seed = 1234)
# 

## ----exir.data, eval=FALSE--------------------------------------------------------------
# # Prepare sample feature names
# gene.names <- paste("gene", 1:2000, sep = "_")
# 
# set.seed(60)
# tp2.vs.tp1.DEGs <- data.frame(
#   logFC = rnorm(n = 700, mean = 2, sd = 4),
#   FDR = runif(n = 700, min = 0.0001, max = 0.049)
# )
# rownames(tp2.vs.tp1.DEGs) <- sample(gene.names, size = 700)
# 
# set.seed(70)
# tp3.vs.tp2.DEGs <- data.frame(
#   logFC = rnorm(n = 1300, mean = -1, sd = 5),
#   FDR = runif(n = 1300, min = 0.0011, max = 0.039)
# )
# rownames(tp3.vs.tp2.DEGs) <- sample(gene.names, size = 1300)
# 
# set.seed(80)
# regression.data <- data.frame(
#   R_squared = runif(n = 800, min = 0.1, max = 0.85)
# )
# rownames(regression.data) <- sample(gene.names, size = 800)

## ----diff_data_assembl, eval=FALSE------------------------------------------------------
# my_Diff_data <- diff_data.assembly(tp2.vs.tp1.DEGs,
#                                    tp3.vs.tp2.DEGs,
#                                    regression.data)
# 
# my_Diff_data[c(1:10),]

## ---------------------------------------------------------------------------------------
Exptl_data_orientation = "features_rows"

## ---------------------------------------------------------------------------------------
normalize = TRUE

## ----exptl_data, eval=FALSE-------------------------------------------------------------
# set.seed(60)
# 
# MyExptl_data <- matrix(
#   data = runif(n = 100000, min = 2, max = 300),
#   nrow = 2000,
#   ncol = 50,
#   dimnames = list(
#     gene.names,
#     c(
#       paste("cancer_sample", 1:25, sep = "_"),
#       paste("normal_sample", 1:25, sep = "_")
#     )
#   )
# )
# 
# # Log-transform the data to mimic normalized log-scale bulk expression values
# MyExptl_data <- log2(MyExptl_data)
# 
# MyExptl_data[1:5, c(1:5, 45:50)] %>% t()

## ----condition.col, eval=FALSE----------------------------------------------------------
# condition <- c(rep("C", 25), rep("N", 25))
# MyExptl_data$condition <- condition

## ----eval=FALSE-------------------------------------------------------------------------
# 
# MyExptl_data_with_condition <- rbind(
#   condition = condition,
#   MyExptl_data
# )
# 
# # In this case, condition = "condition"
# 

## ---------------------------------------------------------------------------------------
pseudo_samples_per_group = 100

## ---------------------------------------------------------------------------------------
feature_filter = TRUE

## ---------------------------------------------------------------------------------------
always_keep_diff_features = TRUE

## ----ExIR, eval=FALSE-------------------------------------------------------------------
# 
# # The table of differential/regression data previously prepared
# my_Diff_data
# 
# # Column indices of differential values in Diff_data
# Diff_value <- c(1, 3)
# 
# # Column index of regression values in Diff_data
# Regr_value <- 5
# 
# # Column indices of significance values in Diff_data
# Sig_value <- c(2, 4)
# 
# # The matrix of normalized experimental data previously prepared
# MyExptl_data
# 
# # The condition vector in the same order as the samples/columns of MyExptl_data
# condition <- c(rep("C", 25), rep("N", 25))
# 
# # Optional desired list of features
# set.seed(60)
# MyDesired_list <- sample(gene.names, size = 500)
# 
# # Run the ExIR model
# My.exir <- exir(
#   Desired_list = MyDesired_list,
#   Diff_data = my_Diff_data,
#   Diff_value = Diff_value,
#   Regr_value = Regr_value,
#   Sig_value = Sig_value,
#   Exptl_data = MyExptl_data,
#   Exptl_data_type = "bulk",
#   condition = condition,
#   Exptl_data_orientation = "features_rows",
#   normalize = FALSE,
#   pseudo_sample = FALSE,
#   feature_filter = TRUE,
#   cor_thresh_method = "mr",
#   mr = 100,
#   seed = 60,
#   verbose = FALSE
# )
# 
# names(My.exir)
# #> [1] "Driver table"         "DE-mediator table"    "Biomarker table"      "Graph"
# 
# class(My.exir)
# #> [1] "ExIR_Result"

## ----eval=FALSE-------------------------------------------------------------------------
# My.exir <- exir(
#   Desired_list = MyDesired_list,
#   Diff_data = my_Diff_data,
#   Diff_value = Diff_value,
#   Regr_value = Regr_value,
#   Sig_value = Sig_value,
#   Exptl_data = raw_count_matrix,
#   Exptl_data_type = "bulk",
#   condition = condition,
#   Exptl_data_orientation = "features_rows",
#   normalize = TRUE,
#   feature_filter = TRUE,
#   cor_thresh_method = "mr",
#   mr = 100,
#   seed = 60,
#   verbose = FALSE
# )

## ----eval=FALSE-------------------------------------------------------------------------
# My.exir.sc <- exir(
#   Desired_list = MyDesired_list,
#   Diff_data = my_Diff_data,
#   Diff_value = Diff_value,
#   Regr_value = Regr_value,
#   Sig_value = Sig_value,
#   Exptl_data = sc_counts,
#   Exptl_data_type = "sc",
#   condition = cell_condition,
#   Exptl_data_orientation = "features_rows",
#   pseudo_sample = TRUE,
#   pseudo_samples_per_group = 100,
#   feature_filter = TRUE,
#   cor_thresh_method = "mr",
#   mr = 20,
#   seed = 60,
#   verbose = FALSE
# )

## ----eval=FALSE-------------------------------------------------------------------------
# My.exir.seurat <- exir(
#   Desired_list = MyDesired_list,
#   Diff_data = my_Diff_data,
#   Diff_value = Diff_value,
#   Regr_value = Regr_value,
#   Sig_value = Sig_value,
#   Exptl_data = seurat_object,
#   Exptl_data_type = "sc",
#   condition = "condition",
#   assay = "RNA",
#   layer = "counts",
#   pseudo_sample = TRUE,
#   pseudo_samples_per_group = 100,
#   feature_filter = TRUE,
#   cor_thresh_method = "mr",
#   mr = 20,
#   seed = 60,
#   verbose = FALSE
# )

## ----eval=FALSE-------------------------------------------------------------------------
# pseudo_sample = FALSE
# normalize = FALSE

## ----exir.vis, eval=FALSE---------------------------------------------------------------
# My.exir.Vis <- exir.vis(exir.results = My.exir,
#                         n = 5,
#                         y.axis.title = "Gene")
# 
# My.exir.Vis

## ----comp_manipulate, eval=FALSE--------------------------------------------------------
# # Select which genes to knockout
# set.seed(60)
# ko_vertices <- sample(igraph::as_ids(V(My.exir$Graph)), size = 5)
# 
# # Select which genes to up-regulate
# set.seed(1234)
# upregulate_vertices <- sample(igraph::as_ids(V(My.exir$Graph)), size = 5)
# 
# Computational_manipulation <- comp_manipulate(exir_output = My.exir,
#                                               ko_vertices = ko_vertices,
#                                               upregulate_vertices = upregulate_vertices,
#                                               beta = 0.5, gamma = 1, no.sim = 100, seed = 1234)

