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Pca worflow integrated #146

Merged
merged 23 commits into from
Dec 11, 2023
Merged

Pca worflow integrated #146

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83319ae
Added checks for workflow to pca and sample correlation.
PaulJonasJost Sep 2, 2023
27f7278
Added function to SourceAll.R
PaulJonasJost Sep 6, 2023
54a02c0
Added workflow to volcano plot.
PaulJonasJost Sep 6, 2023
4773e31
Added workflow to heatmap plot.
PaulJonasJost Sep 7, 2023
901f74b
Added workflow to significance analysis and res_tmp/par_tmp.
PaulJonasJost Sep 15, 2023
06626c7
Added workflow to enrichment analysis and res_tmp/par_tmp.
PaulJonasJost Sep 15, 2023
9a510c4
Fixed spelling
PaulJonasJost Sep 15, 2023
23a5919
OA Workflow and res/par_tmp
PaulJonasJost Sep 15, 2023
d6f837d
Displaying mre information on sigAna table
PaulJonasJost Sep 18, 2023
01f4c0c
Calculating log2Foldchanges, table very similar to DESeq Table
PaulJonasJost Sep 21, 2023
dc1dca2
Added panel for volcano plot
PaulJonasJost Sep 21, 2023
30ea0a8
only filter volcano wokrs, both to report and saving plots works.
PaulJonasJost Sep 22, 2023
0761a74
Small change, s.t. legend is on the left side now.
PaulJonasJost Sep 22, 2023
8dea1b6
Working for log transform now as well
PaulJonasJost Sep 22, 2023
0dfda29
Working for DESeq data as well.
PaulJonasJost Sep 24, 2023
a03a95b
Added gridExtra as dependencie. Needs to be put into renv as well.
PaulJonasJost Sep 24, 2023
2caa4d6
Removed volcano plot panel. Do we need to rename "significance Analys…
PaulJonasJost Sep 24, 2023
2d1e4fc
Fixed UpsetPlots
PaulJonasJost Sep 29, 2023
90c2222
Set up Infrastructure for helpfiles
PaulJonasJost Sep 29, 2023
4a664ab
Made gridExtra as an import library.
PaulJonasJost Oct 5, 2023
61dd48b
Merge branch 'develop' into pca_worflow_integrated
PaulJonasJost Oct 5, 2023
fa45576
not deleting png out of www
PaulJonasJost Oct 5, 2023
d98116c
Apply suggestions from code review
PaulJonasJost Dec 11, 2023
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3 changes: 1 addition & 2 deletions program/shinyApp/R/SourceAll.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
source("R/fun_filterRNA.R",local = T)
source("R/fun_LFC.R",local = T)
source("R/fun_volcano.R",local = T)
source("R/fun_popupModal.R",local = T)
source("R/heatmap/fun_entitieSelection.R",local = T)
source("R/fun_savePheatmap.R",local = T)
Expand All @@ -16,7 +15,7 @@ source("R/enrichment_analysis/translation.R", local = T)
source("R/enrichment_analysis/server.R", local = T)
source("R/heatmap/server.R",local = T)
source("R/pca/server.R", local = T)
source("R/volcano_plot/server.R", local = T)
source("R/pca/util.R", local = T)
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Do we want to name it utils.Rto be consistent with all utils files?

source("R/single_gene_visualisation/server.R",local = T)
source("R/sample_correlation/server.R", local = T)
source("R/significance_analysis/server.R", local = T)
Expand Down
20 changes: 10 additions & 10 deletions program/shinyApp/R/data_selection/ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ data_selection_sidebar_panel <- sidebarPanel(
),
div(
class = "DataSelection",
h4("Row selection - biochemical entities"),
h4("Row selection - biochemical entities") %>% helper(type = "markdown", content = "DataSelection_RowSelection"),
uiOutput(outputId = "providedRowAnnotationTypes_ui"),
uiOutput(outputId = "row_selection_ui"),
uiOutput(outputId = "propensityChoiceUser_ui")
Expand Down Expand Up @@ -58,38 +58,38 @@ data_selection_main_panel <- mainPanel(
actionButton(
inputId = "Reset",
label = "Reset"
),
) %>% helper(type = "markdown", content = "DataSelection_Reset"),
NULL
),
hr(style = "border-top: 2px solid #90DBF4;"),
a(id = "toggleAdvanced",
"Data Upload via file input",
style = "background-color: #90DBF4; color: black; padding: 7px 10px; "
),
) %>% helper(type = "markdown", content = "DataSelection_DataUploadFileInput"),
shinyjs::hidden(
div(
id = "advanced",
splitLayout(
style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
uiOutput(outputId = "data_matrix1_ui"),
uiOutput(outputId = "data_sample_anno1_ui")
uiOutput(outputId = "data_matrix1_ui") %>% helper(type = "markdown", content = "DataSelection_Matrix"),
uiOutput(outputId = "data_sample_anno1_ui") %>% helper(type = "markdown", content = "DataSelection_SampleAnno")
),
splitLayout(
style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
uiOutput(outputId = "data_row_anno1_ui"),
uiOutput(outputId = "data_row_anno1_ui") %>% helper(type = "markdown", content = "DataSelection_RowAnno"),
uiOutput(
outputId = "data_preDone_ui"
) %>% helper(type = "markdown", content = "SummarizedExp_help")
) %>% helper(type = "markdown", content = "DataSelection_SummarizedExp")
)
)
),
hr(style = "border-top: 2px solid #90DBF4;"),
uiOutput(outputId = "metadataInput_ui"),
uiOutput(outputId = "metadataInput_ui") %>% helper(type = "markdown", content = "DataSelection_MetaData"),
hr(style = "border-top: 2px solid #90DBF4;"),
downloadButton(
outputId = "SaveInputAsList",
label = "Save file input to upload later"
) %>% helper(type = "markdown", content = "compilation_help"),
) %>% helper(type = "markdown", content = "DataSelection_compilation_help"),
htmlOutput(outputId = "debug", container = pre),
HTML(text = "<br>"),
HTML(text = "<br>")),
Expand All @@ -99,7 +99,7 @@ data_selection_main_panel <- mainPanel(
actionButton(
inputId = "DoVisualDataInspection",
label = "Upload data for visual inspection"
),
) %>% helper(type = "markdown", content = "DataSelection_UploadInspection"),
splitLayout(
style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
DT::dataTableOutput("DataMatrix_VI"),
Expand Down
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