Hello. I have been using maSigPro to analyze a RNA-seq time-course experiment with six time points and two different stimulatory conditions. Mostly the package is working well however I am having some issues with how the see.genes function (and by extension PlotGroups) plots the fit of the gene clusters. The plot produced provide only one point as a label on the x-axis and this point is not even part of the time series. For the time series see the below provided experimental design matrix:

                      Time    Replicate Control Treatment
Th_0_A                 0.0         1       1         0
Th_0_B                 0.0         2       1         0
Th_0_C                 0.0         3       1         0
Th_0.5_A               0.5         1       1         0
Th_0.5_B               0.5         2       1         0
Th_0.5_C               0.5         3       1         0
Th_1_A                 1.0         1       1         0
Th_1_B                 1.0         2       1         0
Th_1_C                 1.0         3       1         0
Th_2_A                 2.0         1       1         0
Th_2_B                 2.0         2       1         0
Th_2_C                 2.0         3       1         0
Th_6_A                 6.0         1       1         0
Th_6_B                 6.0         2       1         0
Th_6_C                 6.0         3       1         0
Th_24_A               24.0         1       1         0
Th_24_B               24.0         2       1         0
Th_24_C               24.0         3       1         0
Th_P_0_A               0.0         1       0         1
Th_P_0_B               0.0         2       0         1
Th_P_0_C               0.0         3       0         1
Th_P_0.5_A             0.5         1       0         1
Th_P_0.5_B             0.5         2       0         1
Th_P_0.5_C             0.5         3       0         1
Th_P_1_A               1.0         1       0         1
Th_P_1_B               1.0         2       0         1
Th_P_1_C               1.0         3       0         1
Th_P_2_A               2.0         1       0         1
Th_P_2_B               2.0         2       0         1
Th_P_2_C               2.0         3       0         1
Th_P_6_A               6.0         1       0         1
Th_P_6_B               6.0         2       0         1
Th_P_6_C               6.0         3       0         1
Th_P_24_A             24.0         1       0         1
Th_P_24_B             24.0         2       0         1
Th_P_24_C             24.0         3       0         1

Some example Data:

                Th_0_A Th_0_B Th_0_C Th_0.5_A Th_0.5_B Th_0.5_C Th_1_A Th_1_B
ENSG00000110514  20385  28618  27895    16344    14116    15943  14923  15888
ENSG00000086015    687   1018   1381     1246     1136     1500    886    782
ENSG00000211769    143    121    113       93      103      111     86     83
ENSG00000211768    128    101     80       64      115      100     87     77
ENSG00000211767    409    329    223      322      303      298    251    240
                Th_1_C Th_2_A Th_2_B Th_2_C Th_6_A Th_6_B Th_6_C Th_24_A
ENSG00000110514  19358  14693  19189  24533   9979   8475  12050   11303
ENSG00000086015   1380    675   1076    632    854    942   2702    4938
ENSG00000211769    111    110     80     81    181    119     87      86
ENSG00000211768     82     91     70    102    106     92     54      61
ENSG00000211767    239    346    290    194    383    239    317     148
                Th_24_B Th_24_C Th_P_0_A Th_P_0_B Th_P_0_C Th_P_0.5_A
ENSG00000110514   10297   11588    30203    30765    35418      34555
ENSG00000086015    4514    5198     3705     3589     4729       4786
ENSG00000211769      78      43      426      606      773        659
ENSG00000211768      36      39      284      409      505        432
ENSG00000211767     104     154     1035      898     1021       1031
                Th_P_0.5_B Th_P_0.5_C Th_P_1_A Th_P_1_B Th_P_1_C Th_P_2_A
ENSG00000110514      30487      34200    27911    26272    31242    26780
ENSG00000086015       3524       4943     3271     3000     3826     3411
ENSG00000211769        698        771      529      567      665      607
ENSG00000211768        502        502      372      402      423      444
ENSG00000211767        993       1020      897      907      980      921
                Th_P_2_B Th_P_2_C Th_P_6_A Th_P_6_B Th_P_6_C Th_P_24_A
ENSG00000110514    23565    27295    16264    17350    18774     17560
ENSG00000086015     2881     3521     4002     3947     4624      8497
ENSG00000211769      787      693      386      432      526       264
ENSG00000211768      531      522      265      253      269       170
ENSG00000211767     1095     1155      701      809      746       498
                Th_P_24_B Th_P_24_C
ENSG00000110514     24385     17360
ENSG00000086015      8765      9009
ENSG00000211769       418       259
ENSG00000211768       229       101
ENSG00000211767       622       309

The plot command:

PlotGroups(data = data, 
           show.fit=TRUE,
           dis=mdesign$dis,
           groups.vector=mdesign$groups.vector,
           edesign=edesign
           )

To get the mdesign matrix do:

mdesign <- make.design.matrix(edesign, degree=5)

I wanted to add the produced plot but I can not figure out how to host it online. Anyway the produced plot only labels x at 5.83333333 and only plots the 24 hour time point. Why? Is there a way to make it plot all time points like it does in the tutorial example? Note that the data provided is not a real cluster however the plot produced has the same problem no matter the underlying data so the problem is most likely in the design matrix.

In case it is important I have the following packages loaded:

library(MASS)
library(maSigPro)
library(edgeR)
library(mclust)
library(ChIPseeker)
library(DOSE)
library(clusterProfiler)
library(ReactomePA)
library(RColorBrewer)
library(ggplot2)
library(ggfortify)
library(stats)
library(gplots)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(data.table)
library(OrganismDbi)
library(org.Hs.eg.db)
library(stringr)