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draw.box_SINBA

draw.box_SINBA.Rd

draw.box_SINBA draws a scatter box plot to visualize one selected seed partner driver single and combined activity values across different phenotype subgroups of samples. Three side-by-side scatter box plots will be created. The left plot shows combined driver paire activity values in different phenotype subgroups, each point is a sample. The middle and right plot shows seed and partner driver activity values in different phenotype subgroups, each point is a sample.

Usage

draw.box_SINBA(
  ac_mat_sinba = NULL,
  ac_mat_single = NULL,
  SINBA_originalID = NULL,
  phenotype_info = NULL,
  group_col = NULL,
  group_levels = NULL,
  group_colors = NULL,
  main = ""
)

Arguments

ac_mat_sinba,

numeric matrix, the activity values of the selected seed-partner driver across all samples.

ac_mat_single,

numeric matrix, the activity values of single driver across all samples

SINBA_originalID,

seed and parterne driver combination, is generated by combineNet2target_list with return_type="SINBA_originalID"

phenotype_info,

a data frame with sample group information

group_col,

character, the column name to be used for group

group_levels,

a vector of characters, the order of the group

group_colors,

a vector of characters, colors to be used for each group

main,

character, the main title of the plot

Examples

ac_mat_sinba<-exprs(SINBA.par$SINBA.ac.eset)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'SINBA.par' not found
ac_mat_single<-exprs(SINBA.par$SINBA_single.ac.eset)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'SINBA.par' not found
SINBA_originalID<-"LCK:STAT3"
phenotype_info<-pData(SINBA.par$SINBA.ac.eset)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'SINBA.par' not found
phenotype_info$condition<-ifelse(phenotype_info$das_lc50>80,"Resistant","Sensitive")
#> Error: object 'phenotype_info' not found
g<-draw.box_SINBA(ac_mat_sinba=ac_mat_sinba,ac_mat_single=ac_mat_single,SINBA_originalID=SINBA_originalID,phenotype_info=phenotype_info,group_col="condition",group_levels=c("Sensitive","Resistant"),group_colors=c("red","blue"))
#> Error in draw.box_SINBA(ac_mat_sinba = ac_mat_sinba, ac_mat_single = ac_mat_single,     SINBA_originalID = SINBA_originalID, phenotype_info = phenotype_info,     group_col = "condition", group_levels = c("Sensitive", "Resistant"),     group_colors = c("red", "blue")): could not find function "draw.box_SINBA"