07-marker-A-individual.Rmd

```{r parameters-and-defaults, include = FALSE}
module <- "scRNAseq"
section <- "marker_genes"
```

```{r parameter-merge, include = FALSE}
local_params <- module %>%
  options() %>%
  magrittr::extract2(module) %>%
  magrittr::extract2(section) %>%
  ReporteR.base::validate_params(parameters_and_defaults)
```

```{r scRNAseq-marker-A-individual-check, include = FALSE, echo = FALSE}
assertive.sets::is_subset(local_params$features, rownames(object_filtered))
if (!is.null(local_params$translate)) {
  assertive.sets::is_subset(local_params$translate, colnames(SummarizedExperiment::rowData(object_filtered)))
}
```

### Individual genes

Figure \@ref(fig:scRNAseq-marker-A-individual-figure) shows selected marker genes **individually**, meaning that the color scale represents the gene expression of a single gene.

```{r scRNAseq-marker-A-individual-figure-params, include = FALSE, echo = FALSE}

theme_marker_individual <- ggplot2::theme(plot.background = ggplot2::element_blank(),
                                 panel.grid.major = ggplot2::element_line(size=.2, colour = "grey"),
                                 panel.grid.minor = ggplot2::element_line(size=.1, colour = "grey"),
                                 panel.border = ggplot2::element_blank(),
                                 panel.background = ggplot2::element_blank(),
                                 axis.line.x = ggplot2::element_line(size=.3),
                                 axis.line.y = ggplot2::element_line(size=.3),
                                 axis.text = ggplot2::element_text(size = 4),
                                 axis.title.y = ggplot2::element_text(size = 5, margin = ggplot2::margin(0, -2, 0, 0)),
                                 axis.title.x = ggplot2::element_text(size = 5, margin = ggplot2::margin(-2, 0, 0, 0)),
                                 legend.text = ggplot2::element_text(size = 4),
                                 legend.title = ggplot2::element_text(size = 5),
                                 plot.title = ggplot2::element_text(face="bold", color="black", size=5),
                                 legend.key.size =  grid::unit(2, "mm"),
                                 legend.margin = ggplot2::margin(b = 2),#grid::unit(-50, "mm"),
                                 legend.position = c(0,1),
                                 legend.justification = c(0,0),
                                 legend.background = ggplot2::element_rect(fill = "white"),
                                 legend.direction = "horizontal")

palette_marker_individual <- c("#D3D3D3", "#FF856D", "#D05C48", "#A13325", "#730000")

if (!length(local_params$translate) == 0) {
  m <- match(local_params$features, rownames(object_filtered))
  assertive.base::assert_any_are_not_na(m)
  feature_names <- SummarizedExperiment::rowData(object_filtered)[m, local_params$translate]
} else {
  feature_names <- local_params$features
}

fig_height <- ReporteR.base::estimate_figure_height(
  height_in_panels = min(ceiling(length(local_params$features)/3), max(4, ceiling(length(local_params$features)/3))),
  panel_height_in_in = params$formatting_defaults$figures$panel_height_in,
  axis_space_in_in = params$formatting_defaults$figures$axis_space_in,
  mpf_row_space = as.numeric(grid::convertUnit(grid::unit(5, 'mm'), 'in')),
  max_height_in_in = params$formatting_defaults$figures$max_height_in)

feature_names_caption <- ReporteR.base::itemize(paste0("(", LETTERS[1:min(12, length(feature_names))], ") ", feature_names[1:min(12, length(feature_names))]))
caption <- glue::glue("Marker gene expression. Samples shown in the 2-dimensional space of *{local_params$dimred}*, color-coded by the expression of {feature_names_caption}.")
```

```{r scRNAseq-marker-A-individual-figure, echo = FALSE, message=FALSE, warning=FALSE, fig.height = fig_height$global, fig.cap = caption}
figure_marker_individual <- multipanelfigure::multi_panel_figure(height = fig_height$sub, columns = min(3, length(local_params$features)), rows = min(ceiling(length(local_params$features)/3), max(4, ceiling(length(local_params$features)/3))), unit = "in")

for(i in 1:min(12, length(local_params$features))) {
  tmp_plot <- object_filtered %>%
    scater::plotReducedDim(use_dimred = local_params$dimred, colour_by = local_params$features[i], add_ticks = FALSE, alpha = 0.9, by_exprs_values = local_params$assay) +
    #ggplot2::guides(colour = FALSE) +
    ggplot2::scale_fill_gradientn(colors = palette_marker_individual, name = feature_names[i]) +
    #ggplot2::scale_color_gradientn(colors = palette_marker_individual) +
    theme_marker_individual
  figure_marker_individual <- multipanelfigure::fill_panel(figure_marker_individual, tmp_plot)
}

figure_marker_individual
```