MIGSAres-plots {MIGSA} | R Documentation |
genesHeatmap
plots a heatmap with the number of experiments in which
each gene contributed to enrich each gene set.
genesBarplot
generates a barplot of the number of gene sets in which
each gene contributed to enrich. Each gene set counts 1 regardless if it was
enriched in many experiments. x-axis each gene, y-axis number of gene sets
in which it contributed to enrich.
migsaHeatmap
plots the enrichment heatmap of the MIGSAres object.
geneSetBarplot
generates a barplot of the number of experiments in
which each gene set was enriched. x-axis each gene set, y-axis times it was
enriched (0 to #experiments).
"MIGSAres-plots"(migsaRes) genesHeatmap(migsaRes, ...) ## S4 method for signature 'MIGSAres' genesHeatmap(migsaRes, enrFilter = 0, gsFilter = 0, colPal = c("white", "red"), col.dist = NA, row.dist = NA, layout = NA, dendrogram = "row") genesBarplot(migsaRes, ...) ## S4 method for signature 'MIGSAres' genesBarplot(migsaRes, enrFilter = 0, gsFilter = 0) migsaHeatmap(migsaRes, ...) ## S4 method for signature 'MIGSAres' migsaHeatmap(migsaRes, enrFilter = 0, expFilter = 0, categories = list(), categLabels = TRUE, colPal = c("white", "red"), col.dist = NA, row.dist = NA, layout = NA, remove0Rows = TRUE, breaks = NA) ## S4 method for signature 'matrix' migsaHeatmap(migsaRes, categories = list(), categLabels = TRUE, colPal = c("white", "red"), col.dist = NA, row.dist = NA, layout = NA) geneSetBarplot(migsaRes, ...) ## S4 method for signature 'MIGSAres' geneSetBarplot(migsaRes, enrFilter = 0)
migsaRes |
MIGSAres object. |
... |
not in use. |
enrFilter |
numeric. Keep gene sets enriched in at least enrFilter experiments. |
gsFilter |
numeric. Keep genes enriched in at least gsFilter gene sets. |
colPal |
vector. Character vector of two colors, first value will represent FALSE/1 on heatmap, and second value TRUE/0. |
col.dist |
character. Distance algorithm to be used in columns, passed to vegdist function. If migsaRes has cutoff then default is jaccard, else, default is euclidean. |
row.dist |
character. Distance algorithm to be used in rows, passed to vegdist function. If migsaRes has cutoff then default is jaccard, else, default is euclidean. |
layout |
matrix. The layout used for heatmaps. |
dendrogram |
character. Wheter to plot "row", "col", "none" or "both" dendrograms. |
expFilter |
numeric. Keep experiments which enriched at least expFilter gene sets. |
categories |
list. List of character vectors, each vector must have the same length as the number of experiments (ncol(migsaRes)-3). It will plot for each category/column a color representing its category. |
categLabels |
logical. Indicates if labels should be plotted for each category. |
remove0Rows |
logical. Whether remove gene sets that are not enriched in any experiment. |
breaks |
numeric. If migsaRes does not have cutoff then break P-values in breaks intervals. |
In heatmap functions: A list returned by heatmap.2 function (plotted data). In other functions: A ggplot object used as graphic.
data(migsaRes); ## For this example lets work with the first 50 results migsaRes <- migsaRes[1:50,]; #### genesHeatmap ## First lets set a cutoff of 0.1 migsaResWCoff <- setEnrCutoff(migsaRes, 0.1); ## Lets check what genes contributed to enrich the highest number of gene ## sets (in more than one gene set). genesHeatmap(migsaResWCoff, gsFilter=1); ## Moreover we can keep gene sets which where enriched in more than ## enrFilter experiments. To do this, we can use the enrFilter parameter. #### genesBarplot ## Lets set a cutoff of 0.01 migsaResWCoff <- setEnrCutoff(migsaRes, 0.01); ## Lets check what genes contributed to enrich the highest number of gene ## sets (in more than one gene set). genesBarplot(migsaResWCoff, gsFilter=1); ## Moreover we can keep gene sets which where enriched in more than ## enrFilter experiments. To do this, we can use the enrFilter parameter. #### migsaHeatmap ## Lets set a cutoff of 0.1 migsaResWCoff <- setEnrCutoff(migsaRes, 0.1); ## Lets visually check enriched gene sets shared between experiments. migsaHeatmap(migsaResWCoff); #### geneSetBarplot ## Lets set a cutoff of 0.1 migsaResWCoff <- setEnrCutoff(migsaRes, 0.1); ## Lets check in how many experiments each gene set was enriched (in more ## than one experiment). geneSetBarplot(migsaResWCoff, enrFilter=1);