GitLab

added plot_title to scatterplot;
added column_title, row_title and option to show column labels to heatmap;
removed double code from AllGenerics.R

Implemented the possibility to color the scatterplot by expression values in the Wrapper;
fixed small bugs in the scatterplot seurat wrapper;
renamed variables in feature_grid_page;
fixed subset_row in feature_expression_page and dimred_feature_page

changed column swapping in barplot.R;
changed page title of dimred_feature_page;
debugged wrapper of feature_expression_page;
subset_row is now obligatory in the heatmap;
removed double code block of plotly_violinplot in visualization_functions;
fixed small colormap bugs in barplot.Rmd, violinplot.Rmd and boxplot.Rmd;

Merge branch 'master' into vignettes

# Conflicts:
#	NAMESPACE
#	R/AllGenerics.R
#	R/dimension_reduction_page.R
#	R/violinplot.R
#	R/visualization_functions.R
#	inst/templates/dimension_reduction_barplot_grouping.Rmd
#	inst/templates/dimension_reduction_dimred.Rmd
#	inst/templates/dimension_reduction_page/barplot_group_sizes.Rmd
#	inst/templates/dimension_reduction_page/metadata_plot.Rmd
#	inst/templates/dimension_reduction_page/scatterplot_dimred.Rmd
#	inst/templates/dimension_reduction_page/silhouette_plot.Rmd
#	inst/templates/dimension_reduction_silhouette.Rmd
#	inst/templates/dimred_sample_page/barplot_group_sizes.Rmd
#	inst/templates/dimred_sample_page/scatterplot_dimred.Rmd
#	inst/templates/dimred_sample_page/silhouette_plot.Rmd
#	man/plotly_violinplot.Rd

Changed comment of switching columns;
exprs_values are converted to matrix;
fixed naming in heatmap Seurat wrapper;
added code{} to description of "..." parameter in visualization_functions.R;
moved images of vignette into /vignettes/images directory

Dimension reduction page

See merge request !26

document wide colormaps

See merge request !24

annotation with provided colormap;
fixed column titles;
set priority of aggregation higher than splitting

Merge branch 'master' into dimension_reduction_page

# Conflicts:
#	NAMESPACE

page with linked dimension reduction and metadata table

See merge request !16

Wrapper gene expression page

See merge request !13

Merge branch 'vignettes' into colormap

# Conflicts:
#	inst/templates/heatmap.Rmd

Merge branch 'master' into vignettes

# Conflicts:
#	NAMESPACE
#	R/AllGenerics.R
#	R/heatmap.R
#	R/scatterplot.R
#	R/visualization_functions.R
#	man/heatmap.Rd
#	man/plotly_scatterplot.Rd
#	man/scatterplot.Rd

heatmap

See merge request !22

switching first two columns in case of equality in barplot.R and scatterplot.R;
implemented document wide colormaps for the primitive functions: boxplot, barplot, violinplot, scatterplot, the components of page dimred_sample_page, added annotation if match with colormap to the heatmap.

small changes in AllGenerics.R

Exported the documentation of several functions to AllGenerics.R;
Changed naming of "reduction_dimension_page" to "dimred_sample_page" and "dimred_metadata_page" to "dimred_feature_page";
Implemented Seurat wrapper for barplot, boxplot, heatmap, scatterplot, violinplot;
Rewritten SingleCellExperiment and Seurat wrapper for dimred_sample_page;
several small debugs.

Merge branch 'wrapper_dimension_reduction_page' into vignettes

# Conflicts:
#	NAMESPACE
#	R/AllGenerics.R
#	R/dimension_reduction_page.R
#	man/add_dim_reduction_page-i2dashboard-Seurat-method.Rd
#	man/add_dim_reduction_page-i2dashboard-SingleCellExperiment-method.Rd
#	man/add_dim_reduction_page-i2dashboard-missing-method.Rd
#	man/dimred-metadata-page.Rd

Merge branch 'heatmap' into vignettes

# Conflicts:
#	NAMESPACE

Merge branch 'wrapper_dimension_reduction_page' of https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq into wrapper_dimension_reduction_page

# Conflicts:
#	NAMESPACE
#	R/AllGenerics.R

Merge branch 'master' into wrapper_dimension_reduction_page

# Conflicts:
#	NAMESPACE

# Conflicts:
#   NAMESPACE

Merge branch 'master' into heatmap

# Conflicts:
#	NAMESPACE

added the code of the example component "bubbleplot" to visualization_functions.R, created a template bubbleplot.Rmd and the validation function bubbleplot.R;
added "shinywidgets" as requirenment to description file;
changed the manpage description of the primitive scatterplot function.

Scatterplot

See merge request !21