################## Testing ssp ######################
library(seqHMM)
### Default settings
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]])
# Multiple stslists
ssplot(hmm_biofam$observations)
# HMM
ssplot(hmm_biofam)
### type = "I"
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I")
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I")
# HMM
ssplot(hmm_biofam, type = "I")
######################### Legends ###############################
### bottom
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.legend = "bottom")
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "bottom")
# HMM
ssplot(hmm_biofam, with.legend = "bottom")
### right.combined
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.legend = "right.combined")
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "right.combined")
# HMM
ssplot(hmm_biofam, with.legend = "right.combined")
### bottom.combined
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.legend = "right.combined")
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "bottom.combined")
# HMM
ssplot(hmm_biofam, with.legend = "bottom.combined")
### ncol.legend
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], ncol.legend = 2)
# Multiple stslists
ssplot(hmm_biofam$observations, ncol.legend = 2)
# HMM
ssplot(hmm_biofam, ncol.legend = 2)
## bottom
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.legend = "bottom", ncol.legend = 2)
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "bottom", ncol.legend = 2)
# HMM
ssplot(hmm_biofam, with.legend = "bottom", ncol.legend = 2)
## right.combined
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "right.combined", ncol.legend = 2)
# HMM
ssplot(hmm_biofam, with.legend = "right.combined", ncol.legend = 2)
# HMM + hidden paths
ssplot(hmm_biofam, plots = "both", with.legend = "right.combined", ncol.legend = 2)
## bottom.combined
# Multiple stslists
ssplot(hmm_biofam$observations, with.legend = "bottom.combined", ncol.legend = 2)
# HMM
ssplot(hmm_biofam, with.legend = "bottom.combined", ncol.legend = 2)
# HMM + hidden paths
ssplot(hmm_biofam, plots = "both", with.legend = "bottom.combined", ncol.legend = 2)
######################### Plots ############################
### HMM
# plots = "both"
ssplot(hmm_biofam, plots = "both")
# plots = "hidden.paths"
ssplot(hmm_biofam, plots = "hidden.paths")
######################### Sorting ############################
### from.start
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.start")
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "from.start")
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.start")
### from.start, hidden paths
# Single-channel stslist (expect error)
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.start", sort.channel = 0)
# Multiple stslists (expect error)
ssplot(hmm_biofam$observations, type = "I", sortv = "from.start", sort.channel = 0)
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.start", sort.channel = 0)
# Hidden paths provided
hp <- (hmm_biofam)
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.start", sort.channel = 0,
hidden.paths = hp)
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "from.start", sort.channel = 0,
hidden.paths = hp)
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.start", sort.channel = 0,
hidden.paths = hp)
### from.start, false channel
# Single-channel stslist (expect error)
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.start", sort.channel = 4)
# Multiple stslists (expect error)
ssplot(hmm_biofam$observations, type = "I", sortv = "from.start", sort.channel = 4)
# HMM (expect error)
ssplot(hmm_biofam, type = "I", sortv = "from.start", sort.channel = 4)
### from.end
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.end")
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "from.end")
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.end")
### from.end, hidden paths
# Hidden paths not provided
# Single-channel stslist (expect error)
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.end", sort.channel = 0)
# Multiple stslists (expect error)
ssplot(hmm_biofam$observations, type = "I", sortv = "from.end", sort.channel = 0)
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.end", sort.channel = 0)
# Hidden paths provided
hp <- (hmm_biofam)
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.end", sort.channel = 0,
hidden.paths = hp)
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "from.end", sort.channel = 0,
hidden.paths = hp)
# HMM
ssplot(hmm_biofam, type = "I", sortv = "from.end", sort.channel = 0,
hidden.paths = hp)
### from.end, false channel
# Single-channel stslist (expect error)
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "from.end", sort.channel = 4)
# Multiple stslists (expect error)
ssplot(hmm_biofam$observations, type = "I", sortv = "from.end", sort.channel = 4)
# HMM (expect error)
ssplot(hmm_biofam, type = "I", sortv = "from.end", sort.channel = 4)
### mds.obs
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "mds.obs")
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "mds.obs")
# HMM
ssplot(hmm_biofam, type = "I", sortv = "mds.obs")
ssplot(hmm_biofam, type = "I", sortv = "mds.obs", plots = "both")
ssplot(hmm_biofam, type = "I", sortv = "mds.obs", plots = "hidden.paths")
### mds.hidden
# Hidden paths not provided
# Single-channel stslist (expect error)
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "mds.hidden")
# Multiple stslists (expect error)
ssplot(hmm_biofam$observations, type = "I", sortv = "mds.hidden")
#####
# Hidden paths provided
hp <- (hmm_biofam)
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = "mds.hidden", hidden.paths = hp)
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = "mds.hidden", hidden.paths = hp)
# HMM
ssplot(hmm_biofam, type = "I", sortv = "mds.hidden")
ssplot(hmm_biofam, type = "I", sortv = "mds.hidden", plots = "both")
ssplot(hmm_biofam, type = "I", sortv = "mds.hidden", plots = "hidden.paths")
### vector
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], type = "I", sortv = 2000:1)
# Multiple stslists
ssplot(hmm_biofam$observations, type = "I", sortv = 2000:1)
# HMM
ssplot(hmm_biofam, type = "I", sortv = 2000:1)
ssplot(hmm_biofam, type = "I", sortv = 2000:1, plots = "both")
ssplot(hmm_biofam, type = "I", sortv = 2000:1, plots = "hidden.paths")
######################### Plot axes ############################
### No x-axis
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], xaxis = FALSE)
# Multiple stslists
ssplot(hmm_biofam$observations, xaxis = FALSE)
# HMM
ssplot(hmm_biofam, xaxis = FALSE)
ssplot(hmm_biofam, xaxis = FALSE, plots = "both")
ssplot(hmm_biofam, xaxis = FALSE, plots = "hidden.paths")
### With y-axis
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], yaxis = TRUE)
# Multiple stslists
ssplot(hmm_biofam$observations, yaxis = TRUE)
# HMM
ssplot(hmm_biofam, yaxis = TRUE)
ssplot(hmm_biofam, yaxis = TRUE, plots = "both")
ssplot(hmm_biofam, yaxis = TRUE, plots = "hidden.paths")
######################### Missing states in legends ############################
### Default settings
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.missing.legend = TRUE)
# Multiple stslists
ssplot(hmm_biofam$observations, with.missing.legend = TRUE)
# HMM
ssplot(hmm_biofam, with.missing.legend = TRUE)
### With missing
# Single-channel stslist
ssplot(hmm_biofam$observations[[1]], with.missing.legend = TRUE, with.missing = TRUE)
# Multiple stslists
ssplot(hmm_biofam$observations, with.missing.legend = TRUE, with.missing = TRUE)
# HMM
ssplot(hmm_biofam, with.missing.legend = TRUE, with.missing = TRUE)
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