Bud fix

export(create_pyscenic_file)

export(data_processing)

export(extract_gene_count)

export(firstup)

export(get_metadata)

export(get_segment)

export(mk_color_table)

  groups,

  add.dot = T,

  font.size=14,

  pt.size=0.1

  pt.size=0.1,

  split.by=NULL

){

  if(is.null(cell.types)){

    cell.types = levels(seu)

  } 

  gene_count<-extract_gene_count(seu=seu, features = feature, cell.types = cell.types, meta.groups = groups)

  gene_count<-extract_gene_count(seu=seu, features = feature, cell.types = cell.types, meta.groups = c(groups, split.by))

  set.seed(seed = 42)

  noise <- rnorm(n = length(x = gene_count[,feature])) / 100000

  gene_count[, feature]<-gene_count[,feature]+noise

      if(add.dot){

        p = p + geom_quasirandom(size=pt.size, alpha=0.2)

      }

      if(!is.null(split.by)){

        p = p + facet_wrap(as.formula(paste("~", split.by)), scales = 'free_x')

      }

      p

    } else {

      if(is.null(split.by)){

        plot_list<-list()

        for(i in 1:length(cell.types)){

          cell_count <- gene_count[gene_count$celltype==cell.types[i],]

          p<-ggplot(cell_count, aes_string(x=groups, y=feature, fill=groups))+

            geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+

            xlab("") + ylab(cell.types[i]) +

            theme(panel.background = element_rect(fill = "white",colour = "black"),

                  legend.position = "none", 

                  axis.text.x = element_blank(), 

        plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] +

          theme(axis.text.x=element_text(angle = 45, hjust = 1, vjust = 1, size = font.size), axis.ticks.x = element_line())

        p<- patchwork::wrap_plots(plotlist = plot_list, ncol = 1)  + patchwork::plot_annotation(title = feature) & theme(plot.title = element_text(hjust = 0.5, size = (font.size +2)))

    }

        p

      } else {

        p<-ggplot(gene_count, aes_string(x = "group", y = feature, fill = "group")) +

          facet_grid(as.formula(paste("celltype","~","group2")), scales = "free_x") +

          geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+

          xlab("") +

          ylab(paste(feature,"expression")) +

          theme_bw() +

          theme(panel.grid.major = element_blank(),

                panel.grid.minor = element_blank(),

                strip.text = element_text( size = font.size),

                axis.text.x = element_text(size=(font.size-2), angle = 45, hjust = 1, vjust = 1),

                axis.title.y = element_text(size = font.size),

                legend.position = "none")

        if(add.dot){

          p = p + geom_quasirandom(size=pt.size, alpha=0.2)

        }

        g <- ggplot_gtable(ggplot_build(p))

        strip_t <- which(grepl('strip-t', g$layout$name))

        strip_r <- which(grepl('strip-r', g$layout$name))

        strip_both<-c(strip_t, strip_r)

        ncol <- length(cell.types) + length(names(table(gene_count[,split.by])))

        fills <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Paired"))(ncol)

        k <- 1

        for (i in strip_both) {

          j <- which(grepl('rect', g$grobs[[i]]$grobs[[1]]$childrenOrder))

          g$grobs[[i]]$grobs[[1]]$children[[j]]$gp$fill <- fills[k]

          k <- k+1

        }

        print(grid::grid.draw(g))

      }

    }

  } else {

    if(!is.null(split.by)){

      stop("This function does not support spliting multiple groups. Plots will look too messy! Please select one group only in the 'groups' parameter if you want to use 'split.by'.")

    }

    if(length(cell.types)==1){

      gene_count<-melt(gene_count[,c(feature, groups)], measure.vars  = groups)

      p<-ggplot(gene_count, aes_string(x="value", y=feature, fill="value"))+

              axis.title = element_text(size = font.size), 

              axis.text.x = element_text(size = font.size, angle = 45, hjust = 1, vjust = 1),

              axis.text.y = element_text(size=(font.size-2)),

              strip.background =element_rect(fill="lemonchiffon1"),

              strip.text = element_text( size = font.size),

              legend.title = element_blank(),

              legend.position = 'none',

              plot.title = element_text(size=(font.size+2), hjust = 0.5))+

    }

  }

}

 No newline at end of file

  feature_count$UMAP2<-umap_data$UMAP_2

  feature_count

}

#' A function to change gene name into first letter capital

#'

#' The function is modified from this thread: https://stackoverflow.com/questions/18509527/first-letter-to-upper-case/18509816

#'

#' @param gene Gene name

#' @export

#' 

firstup <- function(

  gene

  ){

  x <- tolower(gene)

  substr(x, 1, 1) <- toupper(substr(x, 1, 1))

  x

}

This package allows users to visualize the single cell data on the R objects or output files generated by the popular tools such as Seurat, Signac, SCENIC, monocle, CellPhoneDB, CellChat etc. It is currently under active development. A vignette will be available soon.

```

# How to install:

# How to install in R:

devtools::install_github("HaojiaWu/plot1cell")

```

  groups,

  add.dot = T,

  font.size = 14,

  pt.size = 0.1

  pt.size = 0.1,

  split.by = NULL

)

}

\arguments{