## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(message=FALSE)
knitr::opts_chunk$set(warning=FALSE)

## -----------------------------------------------------------------------------
invisible(lapply(
  c("ExpressionAtlas", "SummarizedExperiment", "SingleCellExperiment", "ggplot2"),
  function(pkg) suppressMessages(library(pkg, character.only = TRUE))
))

## ----eval=FALSE---------------------------------------------------------------
# atlas_res <- searchAtlasExperiments( query = "salt", secondaryFilter = "oryza" )
# # Searching for experiments matching your query ...
# # Query successful.
# # Found 4 experiments matching your query.

## ----echo=FALSE---------------------------------------------------------------
data( "atlasRes" )

## -----------------------------------------------------------------------------
atlasRes

## -----------------------------------------------------------------------------
searchAtlasExperiments( query = "lung" , detailed = FALSE )

## -----------------------------------------------------------------------------
searchAtlasExperiments( query = "lung" , detailed = TRUE )

## -----------------------------------------------------------------------------
searchAtlasExperiments( query = "lung", secondaryFilter = "human", detailed = FALSE )

searchAtlasExperiments( query = "lung", secondaryFilter = "human", detailed = TRUE )

## ----eval=FALSE---------------------------------------------------------------
# allExps <- getAtlasData( atlasRes$Accession )
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-GEOD-11175/E-GEOD-11175-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-GEOD-11175
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-MTAB-1625
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1624/E-MTAB-1624-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-MTAB-1624

## ----echo=FALSE---------------------------------------------------------------
data( "allExps" )

## -----------------------------------------------------------------------------
allExps

## ----eval=FALSE---------------------------------------------------------------
# rnaseqExps <- getAtlasData(
#     atlasRes$Accession[
#         grep(
#             "rna-seq",
#             atlasRes$Type,
#             ignore.case = TRUE
#         )
#     ]
# )
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-MTAB-1625

## ----echo=FALSE---------------------------------------------------------------
data( "rnaseqExps" )

## -----------------------------------------------------------------------------
rnaseqExps

## -----------------------------------------------------------------------------
mtab1624 <- allExps[[ "E-MTAB-1624" ]]
mtab1625 <- allExps[[ "E-MTAB-1625" ]]

## -----------------------------------------------------------------------------
sumexp <- mtab1625$rnaseq
sumexp

## -----------------------------------------------------------------------------
head( assays( sumexp )$counts )

## -----------------------------------------------------------------------------
colData( sumexp )

## -----------------------------------------------------------------------------
metadata( sumexp )

## -----------------------------------------------------------------------------
names( mtab1624 )
affy126data <- mtab1624[[ "A-AFFY-126" ]]
affy126data

## -----------------------------------------------------------------------------
head( exprs( affy126data ) )

## -----------------------------------------------------------------------------
pData( affy126data )

## -----------------------------------------------------------------------------
preproc( experimentData( affy126data ) )

## ----eval=FALSE---------------------------------------------------------------
# mtab3007 <- getAtlasExperiment( "E-MTAB-3007" )
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-3007/E-MTAB-3007-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-MTAB-3007

## ----eval=FALSE---------------------------------------------------------------
# mtab4045_tpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "tpm" )
# # Downloading XML file from FTP...
# # E-MTAB-4045  is  rnaseq_mrna_baseline , will continue downloading data
# # Downloading expression file from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-4045/E-MTAB-4045-tpms.tsv
# # Downloading XML file from FTP...

## ----eval=FALSE---------------------------------------------------------------
# mtab4045_cpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "cpm" )
# # Downloading XML file from FTP...
# # E-MTAB-4045  is  rnaseq_mrna_baseline , will continue downloading data
# # Downloading Expression Atlas experiment summary from:
# #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-4045/E-MTAB-4045-atlasExperimentSummary.Rdata
# # Successfully downloaded experiment summary object for E-MTAB-4045

## ----eval=FALSE---------------------------------------------------------------
# mtab10104_dea <- getAnalyticsDifferentialAtlasExpression( "E-MTAB-10104" )
# # Downloading expression file from:
# # ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-10104/E-MTAB-10104-analytics.tsv

## ----eval=TRUE, fig.width=7, fig.height=8-------------------------------------
mtab4045_tpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "tpm" ) 
mtab4045 <- heatmapAtlasExperiment( df = mtab4045_tpm, save_pdf = FALSE, show_plot = TRUE, palette = "viridis", top_n = 20, scaled = FALSE, show_heatmap_title = TRUE )


## ----eval=TRUE, fig.width=7, fig.height=8-------------------------------------
mtab4045_cpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "cpm" ) 
mtab4045 <- heatmapAtlasExperiment( df = mtab4045_cpm, save_pdf = FALSE, show_plot = TRUE,  palette = "viridis", top_n = 20, scaled = TRUE, show_heatmap_title = TRUE )

## ----eval=TRUE, fig.width=7, fig.height=5-------------------------------------
mtab10104_dea <- getAnalyticsDifferentialAtlasExpression( "E-MTAB-10104" )

head(mtab10104_dea)
mtab10104 <-  volcanoDifferentialAtlasExperiment( df = mtab10104_dea, save_pdf = FALSE, show_plot = TRUE, low_fc_colour = "Gray", high_fc_colour = "Blue", cutoff = 1, show_volcanoplot_title = TRUE )


## -----------------------------------------------------------------------------
search_1 <- searchSCAtlasExperiments( query = "endoderm" )
print(search_1)

search_2 <- searchSCAtlasExperiments( query = "endoderm", secondaryFilter = "human" )
print(search_2)

search_3 <- searchSCAtlasExperiments( query = "endoderm", secondaryFilter = "mouse" )
print(search_3)

search_4 <- searchSCAtlasExperiments( query = "arabidopsis" )
print(search_4)

search_5 <- searchSCAtlasExperiments( query = "pluripotency" )
print(search_5)


## ----eval=FALSE---------------------------------------------------------------
# enad19 <- getAtlasSCExperiment( "E-ENAD-19" )
# # returns a SingleCellExperiment object
# 

## -----------------------------------------------------------------------------
egeod36552 <- getAtlasSCExperiment( "E-GEOD-36552" )
# returns a SingleCellExperiment object

print("Reduced dimension names:")
print(reducedDimNames(egeod36552))

print("Column data names:")
print(colnames(colData(egeod36552)))

plotDimRedSCAtlasExperiment(egeod36552, dimRed = "X_pca", colorby = "time" )

plotDimRedSCAtlasExperiment(egeod36552, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "cell_type")

plotDimRedSCAtlasExperiment(egeod36552, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "louvain_resolution_2.0") + theme_classic() + theme(legend.position = "left")


## -----------------------------------------------------------------------------
egeod36552 <- getAtlasSCExperiment( "E-GEOD-36552" )

heatmapSCAtlasExperiment( egeod36552, genes=NULL, sel.K=NULL, scaleNormExp=TRUE, show_row_names=FALSE ) 

# heatmapSCAtlasExperiment( egeod36552, genes=NULL, sel.K=NULL, scaleNormExp=TRUE, show_row_names=FALSE ) 

heatmapSCAtlasExperiment( egeod36552, genes=NULL, sel.K=6, scaleNormExp=TRUE, show_row_names=FALSE ) 


## -----------------------------------------------------------------------------
egeod36552 <- getAtlasSCExperiment( "E-GEOD-36552" )

heatmapSCAtlasExperiment( egeod36552, genes=c('ENSG00000151611','ENSG00000020577', 'ENSG00000188869' ), sel.K=NULL, scaleNormExp=FALSE, show_row_names=TRUE ) 

# heatmapSCAtlasExperiment( egeod36552, genes=c('ENSG00000151611','ENSG00000020577', 'ENSG00000188869' ), sel.K=NULL, scaleNormExp=TRUE, show_row_names=TRUE ) 


## ----fig.width=7, fig.height=4------------------------------------------------
egeod36552 <- getAtlasSCExperiment( "E-GEOD-36552" )

# dotPlotSCAtlasExperiment(egeod36552, genes=c('ENSG00000166681','ENSG00000178928', 'ENSG00000142182' , 'ENSG00000160282' ), sel.K=4)

dotPlotSCAtlasExperiment(egeod36552, genes=c('ENSG00000166681','ENSG00000178928', 'ENSG00000142182' , 'ENSG00000160282' ), sel.K=4, scaleNormExp=TRUE) + theme_classic()

## -----------------------------------------------------------------------------
sessionInfo()