View source: R/plotMultipleGS.R
plotMultipleGS | R Documentation |
This function can plot different representations of the gene expression in a list of gene sets.
plotMultipleGS( genesets_list, ncolumns = 1, labels = NULL, expr, gmt, Subject_ID, TimePoint, baseline = NULL, group.var = NULL, Group_ID_paired = NULL, ref = NULL, group_of_interest = NULL, FUNcluster = NULL, clustering_metric = "euclidian", clustering_method = "ward", B = 500, max_trends = 4, aggreg.fun = "median", na.rm.aggreg = TRUE, trend.fun = "median", methodOptiClust = "firstSEmax", indiv = "genes", verbose = TRUE, clustering = TRUE, showTrend = TRUE, smooth = TRUE, time_unit = "", y.lab = NULL, desc = TRUE, lab.cex = 1, axis.cex = 1, main.cex = 1, y.lab.angle = 90, x.axis.angle = 45, margins = 1, line.size = 1, y.lim = NULL, x.lim = NULL, gg.add = list(), show_plot = TRUE )
genesets_list |
a list of the character strings giving the names of the
gene sets to be plotted as they appear in |
ncolumns |
the number of columns used to display the multiple plots.
Default is |
labels |
List of labels to be added to the plots.
You can also set |
expr |
either a matrix or dataframe of gene expression upon which
dynamics are to be calculated, or a list of gene sets estimation of gene
expression. In the case of a matrix or dataframe, its dimension are n
x p, with the p sample in column and the n genes in row.
In the case of a list, its length should correspond to the number of gene
sets under scrutiny and each element should be an 3 dimension array of
estimated gene expression, such as for the list returned in the
|
gmt |
a gmt object containing the gene sets definition. See
|
Subject_ID |
a factor of length p that is in the same order as the
columns of |
TimePoint |
a numeric vector or a factor of length p that is in
the same order as |
baseline |
a character string which is the value of |
group.var |
in the case of several treatment groups, this is a factor of
length p that is in the same order as |
Group_ID_paired |
a character vector of length p that is in the
same order as |
ref |
the group which is used as reference in the case of several
treatment groups. Default is |
group_of_interest |
the group of interest, for which dynamics are to be
computed in the case of several treatment groups. Default is |
FUNcluster |
a function which accepts as first argument a matrix
|
clustering_metric |
character string specifying the metric to be used
for calculating dissimilarities between observations in the hierarchical
clustering when |
clustering_method |
character string defining the agglomerative method
to be used in the hierarchical clustering when |
B |
integer specifying the number of Monte Carlo ("bootstrap") samples
used to compute the gap statistics. Default is |
max_trends |
integer specifying the maximum number of different clusters
to be tested. Default is |
aggreg.fun |
a character string such as |
na.rm.aggreg |
a logical flag indicating whether |
trend.fun |
a character string such as |
methodOptiClust |
character string indicating how the "optimal" number
of clusters is computed from the gap statistics and their standard
deviations. Possible values are |
indiv |
a character string indicating by which unit observations are
aggregated (through |
verbose |
logical flag enabling verbose messages to track the computing
status of the function. Default is |
clustering |
logical flag. If |
showTrend |
logical flag. If |
smooth |
logical flag. If |
time_unit |
the time unit to be displayed (such as |
y.lab |
character specifying the annotation of the y axis. If |
desc |
a logical flag. If |
lab.cex |
a numerical value giving the amount by which lab labels text
should be magnified relative to the default |
axis.cex |
a numerical value giving the amount by which axis annotation
text should be magnified relative to the default |
main.cex |
a numerical value giving the amount by which title text
should be magnified relative to the default |
y.lab.angle |
a numerical value (in [0, 360]) giving the orientation by
which y-label text should be turned (anti-clockwise). Default is |
x.axis.angle |
a numerical value (in [0, 360]) giving the orientation by
which x-axis annotation text should be turned (anti-clockwise). Default is
|
margins |
a numerical value giving the amount by which the margins
should be reduced or increased relative to the default |
line.size |
a numerical value giving the amount by which the line sizes
should be reduced or increased relative to the default |
y.lim |
a numeric vector of length 2 giving the range of the y-axis.
See |
x.lim |
if numeric, will create a continuous scale, if factor or
character, will create a discrete scale. Observations not in this range will
be dropped. See |
gg.add |
A list of instructions to add to the |
show_plot |
logical flag. If |
If expr
is a matrix or a dataframe, then the "original" data are
plotted. On the other hand, if expr
is a list returned in the
'Estimations'
element of TcGSA.LR
, then it is those
"estimations" made by the TcGSA.LR
function that are plotted.
If indiv
is 'genes', then each line of the plot is the median of a
gene expression over the patients. On the other hand, if indiv
is
'patients', then each line of the plot is the median of a patient genes
expression in this gene set.
This function uses the Gap statistics to determine the optimal number of
clusters in the plotted gene set. See
clusGap
.
A list with 2 elements:
classif
: a data.frame
with the 2 following variables: ProbeID
which
contains the IDs of the probes of the plotted gene set, and Cluster
containing $
which cluster the probe belongs to. If clustering
is FALSE
, then Cluster
is NA
for all the probes.
p
: a ggplot
object containing the plot
Boris P. Hejblum
ggplot
, clusGap
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