Alessandro Aiezza aaiezza
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| #!/usr/bin/Rscript | |
| ## Properties | |
| FRM_GENE_FILE <- 'frm_gene_exp.diff.txt' | |
| FAV_COLS <- c( 'gene', 'sample_1', 'sample_2', 'value_1', 'value_2', 'log2(fold_change)', 'q_value' ) | |
| GENE_ID_FILTER <- '^((Mir([\\d]|let)+.*)|---|LOC\\d+|(.*Rik.*))$' | |
| HEATMAPS_DIR <- 'heatmaps' | |
| VOLCANO_WIDGET_DIR <- 'interactiveVolcanoPlots' | |
| ## Package Dependencies |
aaiezza
/ RNA-Seq_plotUtils.R
Created
June 29, 2017 17:06
Miscellaneous functions used for plotting gene data.
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| #!/usr/bin/Rscript | |
| suppressMessages( library( calibrate ) ) | |
| suppressMessages( library( ggplot2 ) ) | |
| suppressMessages( library( ggrepel ) ) | |
| suppressMessages( library( ggdendro ) ) | |
| suppressMessages( library( dendextend ) ) | |
| suppressMessages( require( htmlwidgets ) ) | |
| suppressMessages( require( gridExtra ) ) | |
| suppressMessages( require( plotly ) ) |
aaiezza
/ plotNorm.R
Created
June 27, 2017 14:15
ggplot2 plotting function for a Normal Distribution with lightly shaded and labeled standard deviations from the mean. User may also give lower and upper bounds, which adds shading under the curve between those points and a label with the area under the curve. (Made to accommodate for Mathematical Statistics with Applications 7th Ed. - WMS 2008)
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| ## | |
| # Standard function for printing Normal Distribution in ggplot2 | |
| # # # # | |
| plotNormCurve <- function( mean = 0, sd = 1, variance = sd ^ 2, | |
| lowerBound = NULL, upperBound = NULL, | |
| sdRange = 3.5, | |
| from = mean - (sdRange * sd), | |
| to = mean + (sdRange * sd), | |
| plotTitle = 'Normal Curve', xlab = 'x', ylab = 'density' | |
| ) |
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