heatmapCmap {cogena} | R Documentation |
heatmapCmap is desgined for the cogena result from CMap only so as to collapse the multi-isntance drugs in CMap!
heatmapCmap(object, method = clusterMethods(object), nCluster = nClusters(object), orderMethod = "max", MultiInstance = "drug", CutoffNumGeneset = 20, CutoffPVal = 0.05, mergeMethod = "mean", low = "grey", high = "red", na.value = "white", maintitle = NULL, printGS = FALSE, add2 = TRUE, geom = "tile") ## S4 method for signature 'cogena' heatmapCmap(object, method = clusterMethods(object), nCluster = nClusters(object), orderMethod = "max", MultiInstance = "drug", CutoffNumGeneset = 20, CutoffPVal = 0.05, mergeMethod = "mean", low = "grey", high = "red", na.value = "white", maintitle = "cogena", printGS = FALSE, add2 = TRUE, geom = "tile")
object |
a genecl or cogena object |
method |
as clMethods in genecl function |
nCluster |
as nClust in cogena function. |
orderMethod |
the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster. |
MultiInstance |
merge multi instances. Options are "drug", "celldrug", "conccelldrug", "concdrug". |
CutoffNumGeneset |
the cut-off of the number of gene sets in the return table. The default is 20. |
CutoffPVal |
the cut-off of p-value. The default is 0.05. |
mergeMethod |
max or mean. The default is mean. |
low |
colour for low end of gradient. |
high |
colour for high end of gradient. |
na.value |
Colour to use for missing values. |
maintitle |
a character. Default is null |
printGS |
print the enriched gene set names or not. Default is FALSE |
add2 |
enrichment score for add Up and Down reuglated genes. |
geom |
tile or circle |
orderMethod:
max. ordered by the max value in clusters beside all
mean. ordered by the mean value in clusters beside all
All. ordered by all genes
Up. ordered by up-regulated genes (add2 should be TRUE)
Down. ordered by down-regulated genes (add2 should be TRUE)
MultiInstance:
drug. merge based on cmap_name
celldrug. merge based on cmap_name and cell type
conccelldrug. merge based on cmap_name, cell type and concentration
a gene set enrichment heatmap
data(Psoriasis) annofile <- system.file("extdata", "CmapDn100.gmt.xz", package="cogena") ## Not run: genecl_result <- coExp(DEexprs, nClust=3, clMethods=c("pam"), metric="correlation", method="complete", ncore=2, verbose=TRUE) clen_res1 <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel) heatmapCmap(clen_res1, "pam", "3", orderMethod="2") heatmapCmap(clen_res1, "pam", "3", orderMethod="2", MultiInstance="concdrug") ## End(Not run)