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Clustering at one LOD score for all markers does usually not result in correct classification of homologues. Usually there are more clusters of (pseudo)homologues than expected. This function lets you inspect every linkage group separately and allows for clustering at a different LOD threshold per LG.
cluster_per_LG(
LG,
linkage_df,
LG_hom_stack,
LOD_sequence,
modify_LG_hom_stack = FALSE,
nclust_out = NULL,
network.layout = c("circular", "stacked", "n"),
device = NULL,
label.offset = 1,
cex.lab = 0.7,
log = NULL,
...
)A modified LG_hom_stack data.frame if modify_LG_hom_stack = TRUE
Integer. Linkage group to investigate.
A data.frame as output of linkage with arguments markertype1 = c(1,0) and markertype2=NULL.
A data.frame with columns "SxN_Marker" providing 1.0 markernames and "LG"
and "homologue" providing linkage group and homologue respectively.
A numeric or vector of numerics giving LOD threshold(s) at which clustering should be performed.
Logical. Should LG_hom_stack be modified and returned?
Number of clusters in the output. If there are more clusters than this number only the nclust_out largest clusters are returned.
Network layout: "circular" or "stacked". If "n" no network is plotted.
Function of the graphics device to plot to (e.g. pdf, png, jpeg). The active device is used when NULL
Offset of labels. Only used if network.layout="circular".
label character expansion. Only for network.layout="circular".
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.
Arguments passed to device.
data("SN_SN_P2", "LGHomDf_P2_1")
#take only markers in coupling:
SN_SN_P2_coupl <- SN_SN_P2[SN_SN_P2$phase=="coupling",]
cluster_per_LG(LG = 2,
linkage_df=SN_SN_P2_coupl,
LG_hom_stack=LGHomDf_P2_1,
LOD_sequence=seq(4,10,2),
modify_LG_hom_stack=FALSE,
nclust_out=4,
network.layout="circular",
device=NULL,
label.offset=1.2,
cex.lab=0.75)
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