scRNA-seq data visualization from scrattch
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README.md

scrattch.vis

Single-cell RNA-seq visualization tools.

This package is under heavy development and optimization.

Seeing into the fishbowl

Installation

All of the dependencies for scrattch.vis are available from CRAN. You can install scrattch.vis from Github using:

install.packages("devtools")
devtools::install_github("AllenInstitute/scrattch.vis")

Plot Types

Once installed, scrattch.vis provides a variety of functions for visualizing scRNA-seq data based on sample annotations. Each of these returns a ggplot2 plot object:

Load packages and data:

library(tasic2016data)
library(scrattch.vis)
options(stringsAsFactors = F)

anno <- tasic_2016_anno
anno <- anno[anno$cluster_id > 0,]
data <- tasic_2016_rpkm
data_df <- cbind(sample_name = colnames(data),
                 as.data.frame(t(data[c("Pvalb","Sst","Rorb"),])))

Sample-centric plots:

sample_bar_plot()

sample_bar_plot(data_df, 
                anno, 
                genes = c("Pvalb","Sst","Rorb"), 
                grouping = "primary_type", 
                group_order = c(1,6,2,9,4),
                log_scale = FALSE,
                font_size = 5,
                label_type = "angle")

sample_heatmap_plot()

sample_heatmap_plot(data_df, 
                    anno, 
                    genes = c("Pvalb","Sst","Rorb"), 
                    grouping = "primary_type", 
                    log_scale = TRUE,
                    font_size = 5)

sample_fire_plot()

sample_fire_plot(data_df, 
                 anno, 
                 genes = c("Pvalb","Sst","Rorb"), 
                 grouping = "primary_type", 
                 log_scale = TRUE,
                 top_value = "lowest",
                 font_size = 5)

Group-centric plots:

group_violin_plot()

group_violin_plot(data_df, 
                  anno, 
                  genes = c("Pvalb","Sst","Rorb"), 
                  grouping = "primary_type", 
                  log_scale = FALSE,
                  font_size = 5,
                  rotate_counts = TRUE)

group_quasirandom_plot()

group_quasirandom_plot(data_df, 
                       anno, 
                       genes = c("Pvalb","Sst","Rorb"), 
                       grouping = "primary_type", 
                       log_scale = FALSE,
                       font_size = 5,
                       rotate_counts = TRUE)

group_dot_plot()

group_dot_plot(data_df, 
               anno, 
               genes = c("Pvalb","Sst","Rorb"), 
               grouping = "primary_type", 
               log_scale = TRUE,
               font_size = 5,
               max_size = 5,
               rotate_counts = TRUE)

group_box_plot()

group_box_plot(data_df, 
               anno, 
               genes = c("Pvalb","Sst","Rorb"), 
               grouping = "primary_type", 
               log_scale = FALSE,
               font_size = 5,
               rotate_counts = TRUE)

group_heatmap_plot()

group_heatmap_plot(data_df, 
                   anno, 
                   genes = c("Pvalb","Sst","Rorb"), 
                   grouping = "primary_type", 
                   stat = "tmean",
                   log_scale = TRUE,
                   font_size = 5,
                   rotate_counts = TRUE)

The scrattch suite

scrattch.vis is one component of the scrattch suite of packages for Single Cell RNA-seq Analysis for Transcriptomic Type CHaracterization from the Allen Institute.

License

The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch.vis/blob/master/LICENSE

Level of Support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/scrattch.vis/blob/master/CONTRIBUTION