plot.TcGSA {TcGSA}

Plot a Gene Set Trends Heatmap.

Description

This function plots a gene sets dynamic trends heatmap.

Usage

## S3 method for class 'TcGSA'
plot(
  x,
  threshold = 0.05,
  myproc = "BY",
  nbsimu_pval = 1e+06,
  expr,
  Subject_ID,
  TimePoint,
  baseline = NULL,
  only.signif = TRUE,
  group.var = NULL,
  Group_ID_paired = NULL,
  ref = NULL,
  group_of_interest = NULL,
  ranking = FALSE,
  FUNcluster = NULL,
  clustering_metric = "euclidian",
  clustering_method = "ward",
  B = 500,
  max_trends = 4,
  aggreg.fun = "median",
  na.rm.aggreg = TRUE,
  methodOptiClust = "firstSEmax",
  indiv = "genes",
  verbose = TRUE,
  clust_trends = NULL,
  N_clusters = NULL,
  myclusters = NULL,
  label.clusters = NULL,
  prev_rowCL = NULL,
  descript = TRUE,
  plot = TRUE,
  color.vec = c("darkred", "#D73027", "#FC8D59", "snow", "#91BFDB", "#4575B4",
    "darkblue"),
  legend.breaks = NULL,
  label.column = NULL,
  time_unit = "",
  cex.label.row = 1,
  cex.label.column = 1,
  margins = c(5, 25),
  heatKey.size = 1,
  dendrogram.size = 1,
  heatmap.height = 1,
  heatmap.width = 1,
  cex.clusterKey = 1,
  cex.main = 1,
  horiz.clusterKey = TRUE,
  main = NULL,
  subtitle = NULL,
  ...
)

Arguments

x

an object of class'TcGSA'.

threshold

the threshold at which the FDR or the FWER should be controlled.

myproc

a vector of character strings containing the names of the multiple testing procedures for which adjusted p-values are to be computed. This vector should include any of the following: "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", "TSBH" or "none". "none" indicates no adjustment for multiple testing. See mt.rawp2adjp for details. Default is "BY", the Benjamini & Yekutieli (2001) step-up FDR-controlling procedure (general dependency structures). In order to control the FWER(in case of an analysis that is more a hypothesis confirmation than an exploration of the expression data), we recommend to use "Holm", the Holm (1979) step-down adjusted p-values for strong control of the FWER.

nbsimu_pval

the number of observations under the null distribution to be generated in order to compute the p-values. Default is 1e+06.

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 'Estimations' element of TcGSA.LR. See details.

Subject_ID

a factor of length p that is in the same order as the columns of expr (when it is a dataframe) and that contains the patient identifier of each sample. Ignored if expr is a list of estimations.

TimePoint

a numeric vector or a factor of length p that is in the same order as Subject_ID and the columns of expr (when it is a dataframe), and that contains the time points at which gene expression was measured. Ignored if expr is a list of estimations.

baseline

the value of TimePoint to be used as baseline. Default is NULL in which case expression is centered and no baseline is used.

only.signif

logical flag for plotting only the significant gene sets. If FALSE, all the gene sets from the gmt object contained in x are plotted. Default is TRUE.

group.var

in the case of several treatment' groups, this is a factor of length p that is in the same order as Timepoint, Subject_ID, sample_name and the columns of expr. It indicates to which treatment group each sample belongs to. Default is NULL, which means that there is only one treatment group. See Details.

Group_ID_paired

a character vector of length p that is in the same order as Timepoint, Subject_ID, sample_name, group.var and the columns of expr. This argument must not be NULL in the case of a paired analysis, and must be NULL otherwise. Default is NULL. See Details.

ref

the group which is used as reference in the case of several treatment groups. Default is NULL, which means that reference is the first group in alphabetical order of the labels of group.var. See Details.

group_of_interest

the group of interest, for which dynamics are to be computed in the case of several treatment groups. Default is NULL, which means that group of interest is the second group in alphabetical order of the labels of group.var. See Details. group_of_interest here~~

ranking

a logical flag. If TRUE, the gene set trends are not hierarchically classified, but ordered by decreasing Likelihood ratios. Default is FALSE.

FUNcluster

the clustering function used to agglomerate genes in trends. Default is NULL, in which a hierarchical clustering is performed via the function agnes, using the metric clustering_metric and the method clustering_method. See clusGap

clustering_metric

character string specifying the metric to be used for calculating dissimilarities between observations in the hierarchical clustering when FUNcluster is NULL. The currently available options are "euclidean" and "manhattan". Default is "euclidean". See agnes. Also, a "sts" option is available in TcGSA. It implements the 'Short Time Series' distance [Moller-Levet et al., Fuzzy Clustering of short time series and unevenly distributed sampling points, Advances in Intelligent Data Analysis V:330-340 Springer, 2003] designed specifically for clustering time series.

clustering_method

character string defining the agglomerative method to be used in the hierarchical clustering when FUNcluster is NULL. The six methods implemented are "average" ([unweighted pair-]group average method, UPGMA), "single" (single linkage), "complete" (complete linkage), "ward" (Ward's method), "weighted" (weighted average linkage). Default is "ward". See agnes.

B

integer specifying the number of Monte Carlo ("bootstrap") samples used to compute the gap statistics. Default is 500. See clusGap.

max_trends

integer specifying the maximum number of different clusters to be tested. Default is 4.

aggreg.fun

a character string such as "mean", "median" or the name of any other statistics function defined that returns a single numeric value. It specifies the function used to aggregate the observations before the clustering. Default is to median. Default is "median".

na.rm.aggreg

a logical flag indicating whether NA should be remove to prevent propagation through aggreg.fun. Can be useful to set to TRUE with unbalanced design as those will generate structural NAs in $Estimations. Default is TRUE.

methodOptiClust

character string indicating how the "optimal"" number of clusters is computed from the gap statistics and their standard deviations. Possible values are "globalmax", "firstmax", "Tibs2001SEmax", "firstSEmax" and "globalSEmax". Default is "firstSEmax". See 'method' in clusGap, Details and Tibshirani et al., 2001 in References.

indiv

a character string indicating by which unit observations are aggregated (through aggreg.fun) before the clustering. Possible values are "genes" or "patients". Default is "genes".

verbose

logical flag enabling verbose messages to track the computing status of the function. Default is TRUE.

clust_trends

object of class ClusteredTrends containing already computed trends for the plotted gene sets. Default is NULL.

N_clusters

an integer that is the number of clusters in which the dynamics should be regrouped. The cutoff of the clustering tree is automatically calculated accordingly. Default is NULL, in which case the dendrogram is not cut and no clusters are identified.

myclusters

a character vector of colors for predefined clusters of the represented gene sets, with as many levels as the value of N_clusters. Default is NULL, in which case the clusters are automatically identified and colored via the cutree function and the N_clusters argument only.

label.clusters

if N_clusters is not NULL, a character vector of length N_clusterss. Default is NULL, in which case if N_clusters is not NULL, clusters are simply labeled with numbers.

prev_rowCL

a hclust object, such as the one return by the present plotting function (see Value) for instance. If not NULL, no clustering is calculated by the present plotting function and this tree is used to represent the gene sets dynamics. Default is NULL.

descript

logical flag indicating that the description of the gene sets should appear after their name on the right side of the plot if TRUE. Default is TRUE. See Details.

plot

logical flag indicating whether the heatmap should be plotted or not. Default is TRUE.

color.vec

a character strings vector used to define the color palette used in the plot. Default is c("#D73027", "#FC8D59","lightyellow", "#91BFDB", "#4575B4").

legend.breaks

a numeric vector indicating the splitting points for coloring. Default is NULL, in which case the break points will be spaced equally and symmetrically about 0.

label.column

a vector of character strings with the labels to be displayed for the columns (i.e. the time points). Default is NULL.

time_unit

the time unit to be displayed (such as "Y", "M", "W", "D", "H", etc) next to the values of TimePoint in the columns labels when label.column is NULL. Default is "".

cex.label.row

a numerical value giving the amount by which row labels text should be magnified relative to the default 1.

cex.label.column

a numerical value giving the amount by which column labels text should be magnified relative to the default 1.

margins

numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively. Default is c(15, 100). See Details.

heatKey.size

the size of the color key for the heatmap fill. Default is 1.

dendrogram.size

the horizontal size of the dendrogram. Default is 1

heatmap.height

the height of the heatmap. Default is 1

heatmap.width

the width of the heatmap. Default is 1

cex.clusterKey

a numerical value giving the amount by which the clusters legend text should be magnified relative to the default 1, when N_clusters is not NULL.

cex.main

a numerical value giving the amount by which title text should be magnified relative to the default 1.

horiz.clusterKey

a logical flag; if TRUE, set the legend for clusters horizontally rather than vertically. Only used if the N_clusters argument is not NULL. Default is TRUE.

main

a character string for an optional title. Default is NULL.

subtitle

a character string for an optional subtitle. Default is NULL.

...

other parameters to be passed through to plotting functions.

Details

On the heatmap, each line corresponds to a gene set, and each column to a time point.

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 descript is FALSE, the second element of margins can be reduced (for instance use margins = c(5, 10)), as there is not so much need for space in order to display only the gene set names, without their description.

If there is a large number of significant gene sets, the hierarchical clustering step repeated for each of them can take a few minutes. To speed things up (especially) when playing with the plotting parameters for having a nice plot, one can run the clustTrend function beforehand, and plug its results in the plot.TcGSA function via the clust_trends argument.

Value

An object of class hclust which describes the tree produced by the clustering process. The object is a list with components:

• merge an n-1 by 2 matrix. Row i of merge describes the merging of clusters at step i of the clustering. If an element j in the row is negative, then observation -j was merged at this stage. If j is positive then the merge was with the cluster formed at the (earlier) stage j of the algorithm. Thus negative entries in merge indicate agglomerations of singletons, and positive entries indicate agglomerations of non-singletons.

• height a set of n-1 real values (non-decreasing for ultrametric trees). The clustering height: that is, the value of the criterion associated with the Ward clustering method.

• order a vector giving the permutation of the original observations suitable for plotting, in the sense that a cluster plot using this ordering and matrix merge will not have crossings of the branches.

• labels the gene set trends name.

• call the call which produced the result clustering:
  hclust(d = dist(map2heat, method = "euclidean"), method = "ward.D2")

• method "ward.D2", as it is the clustering method that has been used for clustering the gene set trends.

• dist.method "euclidean", as it is the distance that has been used for clustering the gene set trends.

• legend.breaks a numeric vector giving the splitting points used for coloring the heatmap. If plot is FALSE, then it is NULL.

• myclusters a character vector of colors for the dynamic clusters of the represented gene set trends, with as many levels as the value of N_clusters. If no dynamic clusters were represented, than this is NULL.

• ddr a dendrogram object with the reordering used for the heatmap. See heatmap.2 function from package gplots.

• gene set.names character vector with the names of the gene sets used in the heatmap.

• clust.trends a ClusteredTrends object.

• clustersExport a data frame with 2 variables containing the two following variables :

  • GeneSet: the gene set trends clustered.

  • Cluster: the dynamic cluster they belong to.

  The data frame is order by the variable Cluster.

• data_plotted: the data matrix represented by the heatmap

Author(s)

Boris P. Hejblum

References

Hejblum BP, Skinner J, Thiebaut R, (2015) Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLOS Comput. Biol. 11(6): e1004310. doi: 10.1371/journal.pcbi.1004310

See Also

TcGSA.LR, hclust

Examples

if(interactive()){
data(data_simu_TcGSA)

tcgsa_sim_1grp <- TcGSA.LR(expr=expr_1grp, gmt=gmt_sim, design=design, 
                          subject_name="Patient_ID", time_name="TimePoint",
                          time_func="linear", crossedRandom=FALSE)
summary(tcgsa_sim_1grp)

plot(x=tcgsa_sim_1grp, expr=tcgsa_sim_1grp$Estimations, 
    Subject_ID=design$Patient_ID, TimePoint=design$TimePoint,
    baseline=1, 
    B=100,
    time_unit="H",
    dendrogram.size=0.4, heatmap.width=0.8, heatmap.height=2, cex.main=0.7
    )
           
tcgsa_sim_2grp <- TcGSA.LR(expr=expr_2grp, gmt=gmt_sim, design=design, 
                          subject_name="Patient_ID", time_name="TimePoint",
                          time_func="linear", crossedRandom=FALSE, 
                          group_name="group.var")
summary(tcgsa_sim_2grp)                             
plot(x=tcgsa_sim_2grp, expr=expr_2grp, 
    Subject_ID=design$Patient_ID, TimePoint=design$TimePoint,
    B=100,
    time_unit="H",
    )
}