NoiseScree {BiBitR} | R Documentation |
Noise Scree Plots
Description
Extract patterns from either a Biclust or BiBitWorkflow object (see Details) and plot the Noise Scree plot (same as plot 4 in BiBitWorkflow
). Additionally, if FisherResult
is available (from RowTest_Fisher
), this info will be added to the plot.
Usage
NoiseScree(result, matrix, type = c("Added", "Total"), pattern = NULL,
noise_select = 0, alpha = 0.05)
Arguments
result |
A Biclust or BiBitWorkflow Object. |
matrix |
Accompanying binary data matrix which was used to obtain |
type |
Either |
pattern |
Numeric vector for which patterns the noise scree plot should be drawn (default = all patterns). |
noise_select |
Should an automatic noise selection be applied and drawn (blue vertical line) on the plot? (Using ad hoc method to find the elbow/kink in the Noise Scree plots)
|
alpha |
If info from the Fisher Exact test is available, which significance level should be used to in the plot (Noise versus Significant Fisher Exact Test rows). (default=0.05) |
Details
- Biclust S4 Object
-
Using the column patterns of the Biclust result, the noise level is plotted versus the number of
"Total"
or"Added"
rows. - BiBitWorkflow S3 Object
-
The merged column patterns (after cutting the hierarchical tree) are extracted from the BiBitWorkflow object, namely the
$info$MergedColPatterns
slot. These patterns are used to plot the noise level versus the number of"Total"
or"Added"
rows.
If information on the Fisher Exact Test is available, then this info will added to the plot (noise level versus significant rows).
Value
NULL
Author(s)
Ewoud De Troyer
Examples
## Not run:
## Prepare some data ##
set.seed(254)
mat <- matrix(sample(c(0,1),5000*50,replace=TRUE,prob=c(1-0.15,0.15)),
nrow=5000,ncol=50)
mat[1:200,1:10] <- matrix(sample(c(0,1),200*10,replace=TRUE,prob=c(1-0.9,0.9)),
nrow=200,ncol=10)
mat[300:399,6:15] <- matrix(sample(c(0,1),100*10,replace=TRUE,prob=c(1-0.9,0.9)),
nrow=100,ncol=10)
mat[400:599,21:30] <- matrix(sample(c(0,1),200*10,replace=TRUE,prob=c(1-0.9,0.9)),
nrow=200,ncol=10)
mat[700:799,29:38] <- matrix(sample(c(0,1),100*10,replace=TRUE,prob=c(1-0.9,0.9)),
nrow=100,ncol=10)
mat <- mat[sample(1:5000,5000,replace=FALSE),sample(1:50,50,replace=FALSE)]
## Apply BiBitWorkflow ##
out <- BiBitWorkflow(matrix=mat,minr=50,minc=5,noise=0.2,cut_type="number",cut_pm=4)
# Make Noise Scree Plot - Default
NoiseScree(result=out,matrix=mat,type="Added")
NoiseScree(result=out,matrix=mat,type="Total")
# Make Noise Scree Plot - Use Automatic Noies Selection
NoiseScree(result=out,matrix=mat,type="Added",noise_select=2)
NoiseScree(result=out,matrix=mat,type="Total",noise_select=2)
## Apply RowTest_Fisher on BiBitWorkflow Object ##
out2 <- RowTest_Fisher(result=out,matrix=mat)
# Fisher output is added to "NoiseScree" plot
NoiseScree(result=out2,matrix=mat,type="Added")
NoiseScree(result=out2,matrix=mat,type="Total")
## End(Not run)