Description Usage Arguments Details Examples
View source: R/CompassStratifiedBackgroundCorrectedProportionsBoxplots.R
Subsets will be plotted in the order in which they appear in the cr_cats matrix. Only subsets which appear in compass.subset.comparisons.result will be plotted. Intended to be shown with the categories legend from the corresponding COMPASS heatmap displayed below.
1 2 3 4 5 6 7 8 9 | boxplotsCompassSubsetBgCorrPropStratified(compass.subset.comparisons.result,
cr_cats, stratifyBy, sampleIDCol, parentSubset, themeBaseSize = 18,
removeGridAndBg = FALSE, showSignificanceBracket = TRUE,
pvalue_fontsize = NULL, axestitle_fontsize = NULL,
axestick_fontsize = NULL, font = NULL, geom_jitter_width = 0.05,
xaxis_title = stratifyBy, dot_size = 0.75, legend_position = c(1,
1), show_points = F, padj_method = "bonferroni", ylim = NULL,
p_alpha = 0.05, stratifyBy_colors = NULL, box_fill_alpha = 0.7,
legend_fontsize = NULL)
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compass.subset.comparisons.result |
The output from a run of COMPASSHelpers::compass.subset.comparisons(). Contains the p-values and background-corrected proportions for each subset. |
cr_cats |
a COMPASSResult categories matrix (cr$fit$categories) with rows defining the order in which you want the boxplots to appear. Can be obtained by a call to COMPASSHelpers::orderHeatmapColumnsByCytokinePresence(), for example. |
stratifyBy |
what metadata column to stratify the boxplots by, e.g. "Status" |
sampleIDCol |
e.g. "PATIENT ID" |
parentSubset |
e.g. "4+" |
ylim |
e.g. c(0,0.01) |
p_alpha |
The alpha level to use for choosing which subsets to plot p-values for |
stratifyBy_colors |
e.g. c("RSTR" = "white", "LTBI" = "black") |
This function is hacked together.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Not run:
compass.subset.comparisons.result <- compass.subset.comparisons(compassResultOrPath=CD4PP1CompassResult,
gsOrGsListOrPath=gs,
parentSubset="4+",
antigenCol="Antigen",
stimAntigen="Peptide Pool 1",
controlAntigen="DMSO",
stratifyBy="Status",
stratifyByValueMinuend = "LTBI",
stratifyByValueSubtrahend = "RSTR",
sampleIDCol="PATIENT ID")
cr_cats <- orderHeatmapColumnsByCytokinePresence(CD4PP1CompassResult, "IFNg",
cats_df_cytokine_order_override = c("CD154", "IL2", "TNF", "CD107a", "IL4", "IL17a", "IFNg"))$fit$categories
boxplotsCompassSubsetBgCorrPropStratified(compass.subset.comparisons.result,
cr_cats,
stratifyBy="Status",
sampleIDCol,
parentSubset,
removeGridAndBg=T,
ylim=c(0, 0.01),
stratifyBy_colors=c("RSTR" = "white", "LTBI" = "black"))
## End(Not run)
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