seqplotMD  R Documentation 
Plot function to render multidomain state sequences by domain and group. The function takes care to make the plots comparable across domains.
seqplotMD(channels,
group = NULL,
type = "i",
main = NULL,
cpal.dom = NULL,
missing.color = NULL,
ylab = NULL,
yaxis = "all",
xaxis = "all",
xtlab = NULL,
stats = "all",
cex.axis = 1,
with.legend = "auto",
ltext.dom = NULL,
cex.legend = 1,
legend.prop = ifelse(dom.byrow,.25,.15),
dom.byrow = FALSE,
dom.crit = 0,
dnames=names(channels),
...)
channels 
List of paired domain state sequence objects. 
group 
Grouping variable of length equal to the number of multidomain sequences. When not 
type 
the type of the plot. Available types are

main 
Character string. Title of the graphic. Default is 
cpal.dom 
List. List of color palettes for the states of each domain. By default, the 
missing.color 
Color for representing missing values inside the sequences. By default, this color is taken for each domain from the 
ylab 
Character string or vector of strings. Optional label of the yaxis. If a vector, yaxis label of each group level. If set as 
yaxis 
Logical or one of 
xaxis 
Logical or one of 
xtlab 
Vector of length equal to the maximal length of the sequences. Optional labels of the xaxis tick labels. If unspecified, column names of the elements of 
stats 
Logical or one of 
cex.axis 
Real value.
Axis annotation magnification. When 
with.legend 
Character string or logical. Should legends of the state colors be plotted? Default value 
ltext.dom 
List. List of vector of character strings of length and order corresponding to the alphabet of the corresponding elements of 
cex.legend 
Real. Legend magnification. See 
legend.prop 
Real in range [0,1]. Proportion of the graphic area devoted to the legends when 
dom.byrow 
Logical. Should domains be displayed by row? 
dom.crit 
Integer in range 
dnames 
String vector. Names of the domains. 
... 
arguments to be passed to the function called to produce the appropriate statistics and the associated plot method (see details), or other graphical parameters. For example, the 
The seqplotMD
function is intended for multidomain (or multichannel) sequences, i.e. situations where each case is represented by a sequence in each of several domains. The elements (set of state sequences) of the channels
list are assumed to be paired. Sequences defined in terms of the expanded alphabet formed by the combination of the domain states are called MD sequences. Although the MD sequences (which can be obtained with seqMD
) may be used for some computations, seqplotMD
does not plot the MD sequences themselves, but the corresponding domain sequences.
For details on the types of plot, see seqplot
.
The function organizes the plot area with either domains in rows, groups in columns, and domain legend on the right of each row, or conversely when dom.byrow=FALSE
. Panel titles are defined as "group level: domain", and are preceded by main
when a main value is provided.
The function takes the matching constraints into account as follows:
 For index plots ("i", "I"
), sequences are displayed in same order for each domain. When a sortv
vector is provided among the ...
list, this same sort order is applied to all domains. If a sortv
method is provided, the sorting is computed on the domain specified by the dom.crit
argument. When there is a which.plot
argument (for type="rf"
) in the ...
list, it cannot be "both"
.
 Likewise, for relative frequency plots ("rf"
) the same order is retained for all domains. The sortv
argument is handled as for "i"
and "I"
, except for sortv="mds"
, in which case the sorting is done using the provided diss
matrix.
 For frequency plots ("f"
), sequences displayed correspond to the most frequent MD sequences.
 For plots of representative sequences ("r"
), the representatives are computed for the provided diss
matrix (generally the distances between the MD sequences) and their representation in each domain are displayed. Likewise, for type="rf"
, the medoids of the equally sized groups are computed using the required diss
matrix.
 When type="mt"
, mean time plot, and there is a bar.labels
argument among the ...
list, bar.labels
should be a list of vector or matrices of bar labels by domain.
No special handling other than the domaingroup titles and the organization of the plot panels is applied to other types ("d","dH","Ht","ms","pc"
).
Gilbert Ritschard
Ritschard, G., T.F. Liao, and E. Struffolino (2023). Strategies for multidomain sequence analysis in social research. Sociological Methodology, 53(2), 288322. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/00811750231163833")}.
seqplot
,
plot.stslist
, seqstatd
, plot.stslist.statd
, seqtab
, plot.stslist.freq
, seqmodst
, plot.stslist.modst
, seqmeant
, plot.stslist.meant
, seqrep
, plot.stslist.rep
, seqrf
,
plot.seqrf
, seqpcplot
, seqMD
.
data(biofam)
## Building one channel per type of event (left, children or married)
cases < 200
bf < as.matrix(biofam[1:cases, 10:25])
children < bf==4  bf==5  bf==6
married < bf == 2  bf== 3  bf==6
left < bf==1  bf==3  bf==5  bf==6
## Building sequence objects
require(colorspace)
m.col < sequential_hcl(2, palette = "PurpOr")
c.col < sequential_hcl(2, palette = "Mint")
l.col < sequential_hcl(2, palette = "OrYel")
child.seq < seqdef(children, weights=biofam[1:cases,"wp00tbgs"], cpal=c.col)
marr.seq < seqdef(married, weights=biofam[1:cases,"wp00tbgs"], cpal=m.col)
left.seq < seqdef(left, weights=biofam[1:cases,"wp00tbgs"], cpal=l.col)
seqdom < list(LeftHome=left.seq,Marr=marr.seq,Child=child.seq)
seqplotMD(seqdom, type="d", group=biofam[1:cases,"sex"], xaxis="bottom")
seqplotMD(seqdom, type="dH", group=biofam[1:cases,"sex"], dom.byrow=TRUE,
xaxis="bottom", yaxis="left")
seqplotMD(seqdom, type="mt", group=biofam[1:cases,"sex"])
seqplotMD(seqdom, type="I", group=biofam[1:cases,"sex"],
xaxis="bottom", sortv="from.end")
## sorting on first domain
seqplotMD(seqdom, type="I", group=biofam[1:cases,"sex"],
xaxis="bottom", sortv="from.start", dom.crit=1)
seqplotMD(seqdom, type="f", group=biofam[1:cases,"sex"],
xaxis="bottom", yaxis="left")
## distances betweem MD sequences
MDseq < seqMD(seqdom, what="MDseq", ch.sep="+")
diss < seqdist(MDseq, method="OM", sm="INDELSLOG")
seqplotMD(seqdom, type="rf", group=biofam[1:cases,"sex"],
xaxis="bottom", sortv="from.end", dom.crit=0, diss=diss, k=10)
seqplotMD(seqdom, type="r", group=biofam[1:cases,"sex"],
xaxis="bottom", dom.crit=0, diss=diss)
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