diff --git a/docs/articles/abserr-celltype-1.png b/docs/articles/abserr-celltype-1.png index 084970e..a01aedf 100644 Binary files a/docs/articles/abserr-celltype-1.png and b/docs/articles/abserr-celltype-1.png differ diff --git a/docs/articles/abserr-celltype-sep-1.png b/docs/articles/abserr-celltype-sep-1.png index d7b0f54..251fb9c 100644 Binary files a/docs/articles/abserr-celltype-sep-1.png and b/docs/articles/abserr-celltype-sep-1.png differ diff --git a/docs/articles/clustering-1.png b/docs/articles/clustering-1.png index ef76bc6..4b0f59e 100644 Binary files a/docs/articles/clustering-1.png and b/docs/articles/clustering-1.png differ diff --git a/docs/articles/corr-pred-1.png b/docs/articles/corr-pred-1.png index 087ebd6..f10e446 100644 Binary files a/docs/articles/corr-pred-1.png and b/docs/articles/corr-pred-1.png differ diff --git a/docs/articles/negative-grad-1.png b/docs/articles/negative-grad-1.png index d692c75..67686c5 100644 Binary files a/docs/articles/negative-grad-1.png and b/docs/articles/negative-grad-1.png differ diff --git a/docs/articles/positive-grad-1.png b/docs/articles/positive-grad-1.png index 4a7c242..8c2f223 100644 Binary files a/docs/articles/positive-grad-1.png and b/docs/articles/positive-grad-1.png differ diff --git a/docs/articles/pred-spatial-1.png b/docs/articles/pred-spatial-1.png index 03f4acf..95bc9ba 100644 Binary files a/docs/articles/pred-spatial-1.png and b/docs/articles/pred-spatial-1.png differ diff --git a/docs/articles/pred-spatial-sep-1.png b/docs/articles/pred-spatial-sep-1.png index 81164d4..b9254f8 100644 Binary files a/docs/articles/pred-spatial-sep-1.png and b/docs/articles/pred-spatial-sep-1.png differ diff --git a/docs/articles/pred-spatial-sep-2.png b/docs/articles/pred-spatial-sep-2.png index 587c75b..30e980e 100644 Binary files a/docs/articles/pred-spatial-sep-2.png and b/docs/articles/pred-spatial-sep-2.png differ diff --git a/docs/articles/pred-spatial-sep-3.png b/docs/articles/pred-spatial-sep-3.png index deaf1c1..d1fd6d4 100644 Binary files a/docs/articles/pred-spatial-sep-3.png and b/docs/articles/pred-spatial-sep-3.png differ diff --git a/docs/articles/pred-spatial-sep-extrinsic-1.png b/docs/articles/pred-spatial-sep-extrinsic-1.png index bc089b7..7017111 100644 Binary files a/docs/articles/pred-spatial-sep-extrinsic-1.png and b/docs/articles/pred-spatial-sep-extrinsic-1.png differ diff --git a/docs/articles/pred-spatial-sep-extrinsic-2.png b/docs/articles/pred-spatial-sep-extrinsic-2.png index 96a276c..a9948e5 100644 Binary files a/docs/articles/pred-spatial-sep-extrinsic-2.png and b/docs/articles/pred-spatial-sep-extrinsic-2.png differ diff --git a/docs/articles/pred-spatial-sep-extrinsic-3.png b/docs/articles/pred-spatial-sep-extrinsic-3.png index 5757e08..9da2933 100644 Binary files a/docs/articles/pred-spatial-sep-extrinsic-3.png and b/docs/articles/pred-spatial-sep-extrinsic-3.png differ diff --git a/docs/articles/realModelExample-hq.html b/docs/articles/realModelExample-hq.html index e577f9a..6fdfa03 100644 --- a/docs/articles/realModelExample-hq.html +++ b/docs/articles/realModelExample-hq.html @@ -187,13 +187,13 @@

Loading data into a Spatia 
## An object of class SpatialDDLS 
 ## Real single-cell profiles:
 ##   1058 features and 14989 cells
-##   rownames: Dgat2 Neil3 Tcf7 ... Tcf7 Rpl19 Rps13 Gimap4 
-##   colnames: ACCCTTGCAAGTAGTA-1-0 ACACCAAGTATGGGAC-1-1 GGAGCAAGTCGCATTA-1-3 ... GGAGCAAGTCGCATTA-1-3 TGTAGACAGCCACTCG-1-1 ATGATCGGTATCAAGA-1-2 CGCATAAGTCAGTCCG-1-3 
+##   rownames: Rps3 Rps7 Tmsb4x ... Tmsb4x Cacna1e Mycl Izumo1r 
+##   colnames: TAACACGAGGAGAGGC-1-2 CCCTAACTCGCGGACT-1-2 CCGATGGTCTGCCTGT-1-2 ... CCGATGGTCTGCCTGT-1-2 GCTACCTAGTTATGGA-1-2 TTTACTGGTGGAATGC-1-1 TGTTACTTCTGAGAAA-1-3 
 ## Spatial experiments:
 ##   1 experiments
 ##   1058 features and 1092 spots
-##   rownames: Arhgef10l Osm Clec4a3 ... Clec4a3 Ccl17 Tcrg-C2 Actg2 
-##   colnames: CTGGCGACATAAGTCC-1-1 GGTGAAGTACAGGGAT-1-1 TATTCCACTCAGCTCG-1-1 ... TATTCCACTCAGCTCG-1-1 TGTGTCGCGAGTTGCA-1-0 GAAGTGATTTATCGTG-1-0 AAATCGTGTACCACAA-1-1 
+##   rownames: Kmo Cd2 Spic ... Spic Gpr141 Klra4 Klrd1 
+##   colnames: CGCGGGAATTAGGCAG-1-1 ATTCAGTAGCAGGGTC-1-0 CGGTTGACCTGGCATA-1-0 ... CGGTTGACCTGGCATA-1-0 CTAATTTCAACAACAC-1-0 TCCCGTCAGTCCCGCA-1-1 TCCGATGACTGAGCTC-1-1 
 ## Project: SpatialDDLS-Proj

In this case, we are only working on 1 spatial transcriptomics dataset, but an arbitrary number of SpatialExperiment @@ -205,19 +205,20 @@

Simulation of mixed transc

Now, we are going to simulate cell composition matrices that will serve to simulate mixed transcriptional profiles with known cell proportions. This is done by the genMixedCellProp function -in which we can control different aspects such as the number of mixed -transcriptional profiles to be generated, the number of cells used to -simulate each mixed profile, etc. These parameters must be decided -depending on the single-cell reference and the available computational +in which we can control different aspects, such as the number of mixed +transcriptional profiles to be generated or the number of cells used to +simulate each mixed profile. These parameters must be decided depending +on the size of the single-cell reference and the available computational resources. For this example, and as standard reference, we will use num.sim.spots = 10000 and n.cells = 50. The -cell type compositions of these mixed profiles will be generated by -three methods:

+cell type composition of these mixed profiles will be generated by three +methods: