plotHR {TNBC.CMS} | R Documentation |
Produces a forest plot of hazard ratios for each gene. Also draws a forest plot of subtype-specific hazard ratios.
plotHR(expr, gene.symbol, pred, time, event, by.subtype = TRUE)
expr |
A |
gene.symbol |
A vector of gene symbols for which hazard ratios are computed. |
pred |
A vector of predicted consensus molecular subtypes. |
time |
A vector of the follow-up time. |
event |
A vector representing survival status (0 = alive, 1 = dead). |
by.subtype |
A logical to determine if subtype-specific hazard ratios are computed (default is TRUE). |
A forest plot of hazard ratios.
# Load gene expression profiles and clinical information of TNBC samples data(GSE25055) DFS.status <- colData(GSE25055)$DFS.status DFS.month <- colData(GSE25055)$DFS.month # Predict consensus molecular subtypes of TNBC samples prediction <- predictCMS(expr = GSE25055) # Forest plot of hazard ratios for input genes plotHR(expr = GSE25055, gene.symbol = c("RECK", "RELN", "EHD4", "PRRX2"), pred = prediction, time = DFS.month, event = DFS.status, by.subtype = FALSE) # Subtype-specific forest plot of hazard ratios for input genes plotHR(expr = GSE25055, gene.symbol = c("RECK", "RELN", "EHD4", "PRRX2"), pred = prediction, time = DFS.month, event = DFS.status, by.subtype = TRUE)