Univariate Report: Differential State based on ‘cond’ column

demo chkv

Contrast and number of results per methods:

Acute vs Conv : limma = 249, lmm = 294, In common = 213

Author

Affiliation

Eugénie Lohmann

CRCM (CiBi Group)

Published

April 29, 2024

Report Parameters

Input parameters
	Sélection
adcode	FALSE
analyse_type	DS
annotation_column	CellSubset
batch	acqdate
cluster_id	cluster_id
col_block	patient_id
conditions	cond
conditions_reference	Acute
fc	1
log_bar	FALSE
min_cells	10
min_samples	22
path	/root/analycyte-projects/demo_chkv/0823ECE7
p_value	0.05
project	demo chkv
rds	dataFE.rds
show_parameters	TRUE
show_summary	TRUE
show_heatmap_on_off	TRUE
sorted	TRUE
transform	FALSE
plot_legends	Gender
cols_design_GLMM_random	shared_col
contrast	Conv

This document has been formated using knitr¹ and quarto².

1 Features summary

Sample table with information on conditions (cond), batch (acqdate), ncells (Number of Cells)

percent.cluster : Percentage of clusters with cells (> 10 cells) in this fcs. see 1

1.0.1 Number of fcs per conditions

Condition-based distribution
Acute	Conv
43	43

Information on metaclusters is grouped in this table with the number of cells and the corresponding description.

n_cells : Number of cells in the cluster.
percent.n_cells : Percentage of total cells in the cluster.
percent.fcs : Percentage of samples with cells (> 10 cells) in this cluster. see 1

A total of 37 markers are included in this analysis report.

Type markers (7): CD19, CD38, CD4, CD45RA, CD54, CD8, CXCR5.

State markers (30): CCR4, CCR5, CCR6, CCR7, CD11b, CD11c, CD123, CD127, CD14, CD141, CD16, CD161, CD1c, CD20, CD209, CD25, CD27, CD3, CD40, CD45, CD56, CD57, CD66b, CD80, CD86, CHIKV, CX3CR1, CXCR3, HLADR, PD1.

2 Presence / Absence data

With a minimum of 10 per cluster.

3 Biological Question

The report is based on the analysis question: cond (parameters: Acute, Conv)

The reference is : Acute

The contrast tested are : Acute vs Conv

cond = Acute (43 fcs ):

1 1758 Acute, 3 1760 Acute, 5 1773 Acute, 7 1785 Acute, 9 1790 Acute, 11 1793 Acute, 13 1794 Acute, 15 1800 Acute, 17 1802 Acute, 19 1822 Acute, 21 1823 Acute, 23 1824 Acute, 25 1857 Acute, 27 1828 Acute, 29 1829 Acute, 31 1838 Acute, 33 1839 Acute, 35 1842 Acute, 37 1844 Acute, 39 1847 Acute, 41 1862 Acute, 43 1863 Acute, 45 1864 Acute, 47 1878 Acute, 49 1879 Acute, 51 1880 Acute, 53 1882 Acute, 55 1885 Acute, 57 1886 Acute, 59 1889 Acute, 61 1890 Acute, 63 1891 Acute, 65 1897 Acute, 67 1910 Acute, 69 1912 Acute, 71 1914 Acute, 73 1918 Acute, 75 1920 Acute, 77 1924 Acute, 79 1937 Acute, 81 1925 Acute, 83 1938 Acute, 85 1948 Acute

cond = Conv (43 fcs ):

2 1758 Conv, 4 1760 Conv, 6 1773 Conv, 8 1785 Conv, 10 1790 Conv, 12 1793 Conv, 14 1794 Conv, 16 1800 Conv, 18 1802 Conv, 20 1822 Conv, 22 1823 Conv, 24 1824 Conv, 26 1857 Conv, 28 1828 Conv, 30 1829 Conv, 32 1838 Conv, 34 1839 Conv, 36 1842 Conv, 38 1844 Conv, 40 1847 Conv, 42 1862 Conv, 44 1863 Conv, 46 1864 Conv, 48 1878 Conv, 50 1879 Conv, 52 1880 Conv, 54 1882 Conv, 56 1885 Conv, 58 1886 Conv, 60 1889 Conv, 62 1890 Conv, 64 1891 Conv, 66 1897 Conv, 68 1910 Conv, 70 1912 Conv, 72 1914 Conv, 74 1918 Conv, 76 1920 Conv, 78 1924 Conv, 80 1937 Conv, 82 1925 Conv, 84 1938 Conv, 86 1948 Conv

4 Materials and methods

Median cell state marker signals per cluster are used to cluster_marker for differential states (DS) within populations.

Cell type refers to relatively stable or permanent features of a cell’s identity, while cell state refers to transient features such as signaling or other functional states or the cell cycle.

The following report provides a turnkey analysis using the diffcyt³ package, differential state tests will be calculated using limma (testDS_limma) and we will use LMM when comp decides to work properly.

Design and parameters between analysis
	limma* 5	LMM* 6
Design	cond, acqdate
Block id	patient_id
Random		/
Fixed		cond
p-value	0.05	0.05
log2FC	1
reference	Ritchie et al. 2015, Nucleic Acids Research	Nowicka et al. (2017), F1000Research
utility	Moderated tests	Rare cell population

See Result table 7 for a comparision matrix.

See Union Graphics 8 for associated vizualisations.

5 limma

6.9% NA results

Markers Absence frequency
	percentage
CCR4	6.9
CCR5	6.9
CCR6	6.9
CCR7	6.9
CD11b	6.9
CD11c	6.9
CD123	6.9
CD127	6.9
CD14	6.9
CD141	6.9
CD16	6.9
CD161	6.9
CD1c	6.9
CD20	6.9
CD209	6.9
CD25	6.9
CD27	6.9
CD3	6.9
CD40	6.9
CD45	6.9
CD56	6.9
CD57	6.9
CD66b	6.9
CD80	6.9
CD86	6.9
CHIKV	6.9
CX3CR1	6.9
CXCR3	6.9
HLADR	6.9
PD1	6.9

Cluster Absence frequency
	percentage
Debris	100
T Cell_unassigned	100

List of the sorted significant limma markers x clusters

Acute vs Conv: Monocyte (CD14+ CD16-)_CD25, Monocyte (CD14+ CD16-)_CCR7, CD4+ T Cell (Effector Memory)_CD45, Monocyte (CD14+ CD16-)_CD209, Monocyte (CD14+ CD16-)_CHIKV, Monocyte (CD14+ CD16-)_CD11c, CD4+ T Cell (Central Memory)_CD45, B Cell (Plasmablast)_CD45, CD4+ T Cell (Treg)_CD45, Monocyte (CD14+ CD16-)_CD123, CD4+ T Cell (Effector Memory)_CD57, Monocyte (CD14- CD16+)_CD45, CD4+ T Cell (Naive)_CD45, Plasmacytoid Dendritic Cell_CD25, CD8+ T Cell (EMRA)_CD45, Monocyte (CD14- CD16+)_CD11c, CD4+ T Cell (Naive)_CD57, NK Cell (CD56+ CD16+)_CCR7, CD4+ T Cell (Central Memory)_CD57, Root_unassigned_CD45, CD8+ T Cell (Naive)_CD45, Monocyte (CD14+ CD16-)_CX3CR1, B Cell (CD27-)_CD3, CD4- CD8- T Cell_CXCR3, Monocyte (CD14+ CD16-)_CD16, Monocyte (CD14+ CD16-)_CD40, CD8+ T Cell (Central Memory)_CD45, Plasmacytoid Dendritic Cell_CD3, CD4+ CD8+ T Cell_CD45, B Cell (Memory)_CD45, B Cell_unassigned_CD45, CD4+ T Cell (Treg)_CD57, Plasmacytoid Dendritic Cell_CCR7, NK Cell (CD56+ CD16-)_CD45, Monocyte (CD14+ CD16-)_CD45, CD8+ T Cell (Effector Memory)_CD45, Monocyte (CD14+ CD16-)_CCR5, B Cell_unassigned_CD57, B Cell (Plasmablast)_CD57, CD8+ T Cell (Naive)_CD57, B Cell (CD27-)_CCR6, CD4- CD8- T Cell_CD45, B Cell (CD27-)_CD1c, Monocyte (CD14+ CD16-)_CD14, Monocyte (CD14- CD16+)_PD1, NK Cell (CD56+ CD16+)_CD3, B Cell (CD27-)_CD20, NK Cell (CD56+ CD16-)_CCR7, NK Cell (CD56+ CD16-)_CD3, CD4+ CD8+ T Cell_CD57, NK Cell (CD56+ CD16+)_CD45, CD8+ T Cell (Naive)_CXCR3, B Cell (Memory)_CD57, Plasmacytoid Dendritic Cell_CD45, CD8+ T Cell (Central Memory)_CD57, CD4+ T Cell (Effector Memory)_CD56, CD4+ T Cell (EMRA)_CD45, Monocyte (CD14+ CD16+)_CD40, CD8+ T Cell (Central Memory)_CXCR3, CM- HLADR+_unassigned_CD40, Monocyte (CD14+ CD16+)_CD123, Monocyte (CD14- CD16+)_CD40, B Cell (Plasmablast)_CXCR3, B Cell_unassigned_CCR7, CM- HLADR+_unassigned_CD123, NK Cell (CD56+ CD16-)_CD25, Monocyte (CD14+ CD16-)_CD57, Plasmacytoid Dendritic Cell_CD123, Monocyte (CD14+ CD16+)_CD11c, B Cell_unassigned_CD56, B Cell (CD27-)_CD45, CD8+ T Cell (EMRA)_CCR7, Monocyte (CD14+ CD16-)_CD141, Monocyte (CD14+ CD16+)_CD45, Plasmacytoid Dendritic Cell_CD161, B Cell (CD27-)_CD16, B Cell (CD27-)_CD57, Plasmacytoid Dendritic Cell_CD57, B Cell (CD27-)_CD127, B Cell (Plasmablast)_CD86, Monocyte (CD14+ CD16-)_CD3, Monocyte (CD14- CD16+)_CD141, Monocyte (CD14+ CD16-)_HLADR, B Cell (Memory)_CXCR3, NK Cell (CD56+ CD16-)_CXCR3, Basophil_CD45, Root_unassigned_CXCR3, CM- HLADR+_unassigned_CD14, Monocyte (CD14+ CD16+)_CD57, Monocyte (CD14- CD16+)_CD123, CD4+ T Cell (Treg)_PD1, Monocyte (CD14+ CD16+)_PD1, B Cell (CD27-)_CD25, B Cell (CD27-)_CD11b, Plasmacytoid Dendritic Cell_CCR5, Dendritic Cell (Type 2, CD1c+)_CD40, Monocyte (CD14- CD16+)_CD57, CD8+ T Cell (EMRA)_CXCR3, CD4+ T Cell (Effector Memory)_CXCR3, Plasmacytoid Dendritic Cell_CD141, CD4+ T Cell (Effector Memory)_CCR4, B Cell (CD27-)_HLADR, B Cell (Memory)_CD86, B Cell (Memory)_CCR6, B Cell_unassigned_CXCR3, B Cell (Plasmablast)_HLADR, B Cell_unassigned_CD11b, B Cell_unassigned_CCR6, Monocyte (CD14+ CD16+)_CCR7, CM- HLADR+_unassigned_CD86, Dendritic Cell (Type 1, CD141+)_CD123, Monocyte (CD14- CD16+)_CCR4, B Cell_unassigned_CD25, Monocyte (CD14- CD16+)_CD14, Plasmacytoid Dendritic Cell_CD40, B Cell_unassigned_CD1c, CD4+ T Cell (Effector Memory)_CD80, Monocyte (CD14+ CD16+)_CHIKV, Dendritic Cell (Type 1, CD141+)_CXCR3, Root_unassigned_CD1c, Dendritic Cell (Type 1, CD141+)_CD1c, CD8+ T Cell (EMRA)_CX3CR1, CD4+ T Cell (Naive)_CD56, B Cell_unassigned_HLADR, Monocyte (CD14+ CD16+)_CD14, Root_unassigned_CD141, NK Cell (CD56+ CD16-)_CD40, CD4+ T Cell (Treg)_CD27, CD4+ T Cell (Central Memory)_CD56, Monocyte (CD14+ CD16-)_CD20, CD4+ T Cell (Effector Memory)_CCR5, NK Cell (CD56+ CD16+)_CD25, B Cell (Plasmablast)_CD20, Dendritic Cell (Type 1, CD141+)_CD141, B Cell (CD27-)_CD56, B Cell (Plasmablast)_CD11b, B Cell (Memory)_CD20, CM- HLADR+_unassigned_CD57, CD8+ T Cell (EMRA)_CD11c, CD8+ T Cell (EMRA)_HLADR, B Cell_unassigned_CD20, CM- HLADR+_unassigned_CD45, B Cell (Memory)_CD1c, Dendritic Cell (Type 1, CD141+)_CD14, B Cell (Memory)_CD16, CD4+ T Cell (Central Memory)_PD1, CD4+ T Cell (EMRA)_CXCR3, B Cell (Plasmablast)_CD27, CD4+ CD8+ T Cell_CD56, Monocyte (CD14- CD16+)_CD20, B Cell_unassigned_CHIKV, Monocyte (CD14+ CD16+)_CD1c, B Cell (Memory)_CD127, Dendritic Cell (Type 1, CD141+)_CD80, Dendritic Cell (Type 1, CD141+)_CD45, CM- HLADR+_unassigned_CXCR3, Monocyte (CD14+ CD16-)_CD86, Root_unassigned_CCR5, CM- HLADR+_unassigned_CD20, CM-_unassigned_CD25, Basophil_CD25, Dendritic Cell (Type 2, CD1c+)_CX3CR1, CD8+ T Cell (Effector Memory)_CCR7, CD4+ CD8+ T Cell_PD1, B Cell (Memory)_CCR4, CD4+ T Cell (Effector Memory)_CD40, CD4+ T Cell (Central Memory)_CD27, NK Cell (CD56+ CD16+)_CX3CR1, NK Cell (CD56+ CD16-)_CCR4, CD8+ T Cell (Effector Memory)_CXCR3, Monocyte (CD14- CD16+)_CD3, Monocyte (CD14- CD16+)_CX3CR1, CD4+ T Cell (Central Memory)_CD127, CM- HLADR+_unassigned_CD25, Dendritic Cell (Type 2, CD1c+)_CD27, B Cell_unassigned_CD27, CM-_unassigned_CD11b, CM- HLADR+_unassigned_CD11b, Plasmacytoid Dendritic Cell_CD11b, CM- HLADR+_unassigned_CD3, Dendritic Cell (Type 1, CD141+)_CD86, CD4+ T Cell (Treg)_CCR4, CM-_unassigned_CD14, Dendritic Cell (Type 2, CD1c+)_CCR4, Monocyte (CD14- CD16+)_CD86, Plasmacytoid Dendritic Cell_CXCR3, CD4+ T Cell (Central Memory)_CXCR3, CD4- CD8- T Cell_CD57, NK Cell (CD56+ CD16+)_CD56, B Cell_unassigned_CD16, Monocyte (CD14+ CD16+)_CD3, Dendritic Cell (Type 1, CD141+)_CD20, CD4+ CD8+ T Cell_CCR7, CD4+ CD8+ T Cell_CD27, CD4+ T Cell (Effector Memory)_HLADR, B Cell (Plasmablast)_CD123, Dendritic Cell (Type 1, CD141+)_CCR6, Monocyte (CD14- CD16+)_CD16, NK Cell (CD56+ CD16+)_CD161, B Cell (Memory)_CD40, B Cell (Plasmablast)_CD40, CM-_unassigned_CD45, CM-_unassigned_HLADR, Dendritic Cell (Type 2, CD1c+)_CHIKV, CM-_unassigned_CD123, Plasmacytoid Dendritic Cell_HLADR, CM-_unassigned_CD11c, Dendritic Cell (Type 2, CD1c+)_CCR7, CM-_unassigned_CD57, CD4+ CD8+ T Cell_CCR4, Dendritic Cell (Type 1, CD141+)_CD57, CD8+ T Cell (Central Memory)_CD127, B Cell (CD27-)_CCR4, Monocyte (CD14+ CD16+)_CD86, CD4- CD8- T Cell_CD27, CD4+ T Cell (Central Memory)_CCR7, B Cell (Memory)_CD25, B Cell_unassigned_CD123, CD4+ T Cell (EMRA)_CD127, CD4+ T Cell (EMRA)_CCR4, CM- HLADR+_unassigned_CD141, B Cell (Plasmablast)_CCR6, CD4+ T Cell (Effector Memory)_CD127, CD8+ T Cell (Central Memory)_CD27, Dendritic Cell (Type 1, CD141+)_CD3, CD8+ T Cell (Effector Memory)_CD25, CD4- CD8- T Cell_HLADR, CM-_unassigned_CD86, Dendritic Cell (Type 2, CD1c+)_CD141, Dendritic Cell (Type 1, CD141+)_CCR4, Monocyte (CD14+ CD16-)_CD11b, Root_unassigned_PD1, CD8+ T Cell (Naive)_CD127, CM- HLADR+_unassigned_CCR4, Dendritic Cell (Type 1, CD141+)_CD11b, Basophil_CD11c, B Cell (Memory)_CCR7, Root_unassigned_CD11c, CD4+ T Cell (Treg)_CCR7, Dendritic Cell (Type 2, CD1c+)_CCR5, NK Cell (CD56+ CD16-)_CD161, Dendritic Cell (Type 1, CD141+)_CCR5, NK Cell (CD56+ CD16-)_HLADR, B Cell (CD27-)_CD40, Monocyte (CD14+ CD16+)_CCR5, Monocyte (CD14- CD16+)_CD11b, CD4+ T Cell (Naive)_CD27, CD4- CD8- T Cell_CD127, Root_unassigned_CD56

5.1 graphics

Volcano

log2(Fold Change) in x-axis.
-log10(adjusted p-adjust) in y-axis.
The number of cells associated with the cluster is indicated by the size of the dot.
“significant_limma” DAC are highlighted in red color; associated cuttofs are a combinaison of :
- absolute log2(FC) > 1.
- adjusted pvalue cutoff : 0.05.

Acute vs Conv

5.1.1 volcano plot

Figure 2: Volcano limma Acute vs Conv

Figure 3: Volcano limma Acute vs Conv

5.1.2 violin plot

Figure 5: Violin Plot DA limma Acute vs Conv

5.1.3 mfi heatmap

Figure 6: Heatmap FDR < 0.05 and abs(log(FC)) > 1 DA limma Acute vs Conv

6 LMM

6.1 graphics

List of the sorted significant lmm markers x clusters

Acute vs Conv: B Cell (CD27-)_CD20, B Cell (CD27-)_CD127, B Cell (CD27-)_CD57, B Cell (CD27-)_CCR6, B Cell (CD27-)_CD16, B Cell (CD27-)_CD3, B Cell (CD27-)_CD45, B Cell (CD27-)_CX3CR1, B Cell (CD27-)_CD1c, B Cell (Memory)_CD57, B Cell (Memory)_CD45, B Cell (Memory)_CCR6, B Cell (Memory)_CXCR3, B Cell (Plasmablast)_CD45, B Cell (Plasmablast)_CD57, B Cell (Plasmablast)_CXCR3, B Cell_unassigned_CD57, B Cell_unassigned_CCR7, B Cell_unassigned_CD56, B Cell_unassigned_CD45, CD4+ CD8+ T Cell_CD45, CD4+ T Cell (Central Memory)_CD57, CD4+ T Cell (Central Memory)_CD45, CD4+ T Cell (Effector Memory)_CD57, CD4+ T Cell (Effector Memory)_CD45, CD4+ T Cell (Effector Memory)_CD56, CD4+ T Cell (EMRA)_CD45, CD4+ T Cell (Naive)_CD57, CD4+ T Cell (Naive)_CD45, CD4+ T Cell (Treg)_CD57, CD4+ T Cell (Treg)_CD45, CD4- CD8- T Cell_CXCR3, CD4- CD8- T Cell_CD45, CD8+ T Cell (Central Memory)_CD57, CD8+ T Cell (Central Memory)_CD45, CD8+ T Cell (Central Memory)_CXCR3, CD8+ T Cell (Effector Memory)_CD45, CD8+ T Cell (EMRA)_CD45, CD8+ T Cell (Naive)_CD57, CD8+ T Cell (Naive)_CD45, CD8+ T Cell (Naive)_CXCR3, CM- HLADR+_unassigned_CD40, CM- HLADR+_unassigned_CD123, CM- HLADR+_unassigned_CD14, Dendritic Cell (Type 2, CD1c+)_CD40, Monocyte (CD14+ CD16+)_CD57, Monocyte (CD14+ CD16+)_CCR7, Monocyte (CD14+ CD16+)_CD11c, Monocyte (CD14+ CD16+)_PD1, Monocyte (CD14+ CD16+)_CD40, Monocyte (CD14+ CD16+)_CHIKV, Monocyte (CD14+ CD16+)_CD123, Monocyte (CD14+ CD16+)_CD14, Monocyte (CD14+ CD16+)_CD45, Monocyte (CD14+ CD16+)_CD1c, Monocyte (CD14+ CD16-)_CD209, Monocyte (CD14+ CD16-)_CCR7, Monocyte (CD14+ CD16-)_CD141, Monocyte (CD14+ CD16-)_CD80, Monocyte (CD14+ CD16-)_CD16, Monocyte (CD14+ CD16-)_CCR5, Monocyte (CD14+ CD16-)_CXCR3, Monocyte (CD14+ CD16-)_CD25, Monocyte (CD14+ CD16-)_CD161, Monocyte (CD14+ CD16-)_CHIKV, Monocyte (CD14+ CD16-)_CD11c, Monocyte (CD14+ CD16-)_CX3CR1, Monocyte (CD14+ CD16-)_CD45, Monocyte (CD14+ CD16-)_CD40, Monocyte (CD14+ CD16-)_CD14, Monocyte (CD14+ CD16-)_CD123, Monocyte (CD14- CD16+)_CD40, Monocyte (CD14- CD16+)_CD11c, Monocyte (CD14- CD16+)_PD1, Monocyte (CD14- CD16+)_CD45, NK Cell (CD56+ CD16+)_CCR7, NK Cell (CD56+ CD16+)_CD3, NK Cell (CD56+ CD16+)_CD45, NK Cell (CD56+ CD16-)_CCR7, NK Cell (CD56+ CD16-)_CXCR3, NK Cell (CD56+ CD16-)_CD25, NK Cell (CD56+ CD16-)_CD3, NK Cell (CD56+ CD16-)_CD45, Plasmacytoid Dendritic Cell_CCR7, Plasmacytoid Dendritic Cell_CD3, Plasmacytoid Dendritic Cell_CD45, Plasmacytoid Dendritic Cell_CD25, Plasmacytoid Dendritic Cell_CD123, Plasmacytoid Dendritic Cell_CD161, Root_unassigned_CD45, B Cell (CD27-)_CD11b, Basophil_CD45, CD4+ T Cell (Treg)_PD1, Plasmacytoid Dendritic Cell_CD40, Plasmacytoid Dendritic Cell_CD57, CD8+ T Cell (EMRA)_CCR7, Dendritic Cell (Type 1, CD141+)_CXCR3, B Cell_unassigned_CD25, B Cell_unassigned_CD161, Dendritic Cell (Type 2, CD1c+)_CCR4, Monocyte (CD14+ CD16-)_PD1, NK Cell (CD56+ CD16+)_CXCR3, Monocyte (CD14- CD16+)_CCR4, Monocyte (CD14+ CD16-)_CD57, Monocyte (CD14+ CD16-)_CD3, B Cell (CD27-)_HLADR, B Cell (Plasmablast)_CD86, Dendritic Cell (Type 2, CD1c+)_CX3CR1, Monocyte (CD14+ CD16+)_CD209, Monocyte (CD14- CD16+)_CD141, Monocyte (CD14- CD16+)_CD14, Dendritic Cell (Type 1, CD141+)_CD123, Plasmacytoid Dendritic Cell_CX3CR1, B Cell_unassigned_CD14, Monocyte (CD14+ CD16-)_HLADR, B Cell (Memory)_CD86, Dendritic Cell (Type 1, CD141+)_CD141, Monocyte (CD14- CD16+)_CCR7, NK Cell (CD56+ CD16-)_CD40, B Cell_unassigned_CCR6, NK Cell (CD56+ CD16+)_CD25, B Cell (CD27-)_CD56, B Cell_unassigned_CXCR3, B Cell (Memory)_CD1c, Monocyte (CD14- CD16+)_CD80, B Cell (CD27-)_CD86, CM- HLADR+_unassigned_CD86, Monocyte (CD14+ CD16-)_CD20, CD4+ T Cell (Effector Memory)_CCR4, CD4+ T Cell (Effector Memory)_CD80, Dendritic Cell (Type 1, CD141+)_CD14, Monocyte (CD14- CD16+)_CD123, Plasmacytoid Dendritic Cell_CCR5, B Cell (Plasmablast)_CD40, CD4+ T Cell (Naive)_CD56, CD4+ T Cell (Naive)_CD141, B Cell_unassigned_CD1c, Dendritic Cell (Type 2, CD1c+)_CD45, B Cell (CD27-)_CD14, CD4+ T Cell (Central Memory)_CD56, Dendritic Cell (Type 2, CD1c+)_CD11c, CD4+ T Cell (Effector Memory)_CXCR3, Dendritic Cell (Type 1, CD141+)_CD1c, CD4+ CD8+ T Cell_CD57, Monocyte (CD14+ CD16-)_CCR6, B Cell (CD27-)_CD25, Basophil_CD25, Root_unassigned_CXCR3, B Cell (Plasmablast)_HLADR, Monocyte (CD14+ CD16-)_CD86, CD8+ T Cell (EMRA)_CXCR3, CD4+ T Cell (Treg)_CD27, NK Cell (CD56+ CD16-)_CD123, Dendritic Cell (Type 2, CD1c+)_CD1c, B Cell (Memory)_CD40, Plasmacytoid Dendritic Cell_CD141, CM- HLADR+_unassigned_CHIKV, Dendritic Cell (Type 1, CD141+)_CD86, B Cell (Memory)_PD1, Dendritic Cell (Type 2, CD1c+)_CCR7, CD8+ T Cell (Effector Memory)_CXCR3, CD8+ T Cell (EMRA)_CX3CR1, Dendritic Cell (Type 1, CD141+)_CD45, B Cell (Plasmablast)_CD20, B Cell (Plasmablast)_CD27, CM-_unassigned_CD25, Dendritic Cell (Type 2, CD1c+)_CD27, CM-_unassigned_CD45, Root_unassigned_CD1c, CM- HLADR+_unassigned_CCR4, NK Cell (CD56+ CD16+)_CX3CR1, B Cell (Memory)_CD127, CM- HLADR+_unassigned_CD80, CM- HLADR+_unassigned_CD20, Dendritic Cell (Type 2, CD1c+)_CD16, B Cell (Memory)_CD20, CD4- CD8- T Cell_CD57, Dendritic Cell (Type 1, CD141+)_CD11b, B Cell_unassigned_CHIKV, CM- HLADR+_unassigned_CD3, CD8+ T Cell (EMRA)_CD40, CD4+ T Cell (Effector Memory)_CD141, Plasmacytoid Dendritic Cell_CD11b, B Cell (Memory)_CD56, B Cell_unassigned_CD27, Monocyte (CD14+ CD16-)_CD56, NK Cell (CD56+ CD16-)_CCR6, B Cell_unassigned_CD11b, CD4+ CD8+ T Cell_CD141, Monocyte (CD14- CD16+)_CD209, CD4+ T Cell (Central Memory)_CD127, Plasmacytoid Dendritic Cell_CXCR3, CD8+ T Cell (EMRA)_CD11c, B Cell (CD27-)_CXCR3, CD4+ T Cell (Central Memory)_CD27, CD4+ T Cell (EMRA)_CXCR3, B Cell (Memory)_CD25, Dendritic Cell (Type 1, CD141+)_CD80, CD4+ T Cell (Central Memory)_CXCR3, CM- HLADR+_unassigned_CD45, CM-_unassigned_CXCR3, Plasmacytoid Dendritic Cell_CD27, B Cell_unassigned_HLADR, CD4+ CD8+ T Cell_CCR7, CD4+ T Cell (Treg)_CD127, B Cell (Plasmablast)_CD141, B Cell (Memory)_CD16, NK Cell (CD56+ CD16-)_CCR4, CD4+ T Cell (Effector Memory)_CD40, CD4- CD8- T Cell_PD1, CD4+ T Cell (Central Memory)_PD1, NK Cell (CD56+ CD16+)_CD56, Dendritic Cell (Type 2, CD1c+)_CHIKV, Plasmacytoid Dendritic Cell_HLADR, B Cell (Plasmablast)_CD11b, B Cell (Memory)_CCR4, CD4+ CD8+ T Cell_CD56, B Cell (Memory)_CHIKV, NK Cell (CD56+ CD16-)_CD27, CM- HLADR+_unassigned_CD57, Dendritic Cell (Type 1, CD141+)_CD40, Dendritic Cell (Type 1, CD141+)_CD20, CD4+ T Cell (Treg)_CCR4, CM- HLADR+_unassigned_CXCR3, Monocyte (CD14+ CD16-)_CD66b, B Cell (CD27-)_CD66b, CD4+ CD8+ T Cell_CD27, Monocyte (CD14- CD16+)_CX3CR1, NK Cell (CD56+ CD16-)_CD14, Root_unassigned_CCR5, CD4+ T Cell (Treg)_CD40, NK Cell (CD56+ CD16-)_CCR5, CM-_unassigned_CCR7, CM- HLADR+_unassigned_CD11b, Monocyte (CD14+ CD16+)_CD3, Monocyte (CD14- CD16+)_CD3, CD4+ CD8+ T Cell_CCR4, CD4+ CD8+ T Cell_PD1, Monocyte (CD14- CD16+)_CD1c, Dendritic Cell (Type 2, CD1c+)_CD11b, Monocyte (CD14- CD16+)_CD27, Monocyte (CD14+ CD16+)_CD80, CD4- CD8- T Cell_CD40, Dendritic Cell (Type 1, CD141+)_CD57, Monocyte (CD14+ CD16+)_CXCR3, CD4+ T Cell (Effector Memory)_CCR5, CD8+ T Cell (Central Memory)_CD11c, CM- HLADR+_unassigned_CD25, Dendritic Cell (Type 2, CD1c+)_HLADR, CD4+ T Cell (Treg)_CD56, CM- HLADR+_unassigned_CD141, CD8+ T Cell (EMRA)_HLADR, Dendritic Cell (Type 2, CD1c+)_CD14, Monocyte (CD14- CD16+)_CD20, CD8+ T Cell (Effector Memory)_CCR7, Dendritic Cell (Type 1, CD141+)_PD1, B Cell (Plasmablast)_CD14, B Cell_unassigned_CD20, CD4+ T Cell (Central Memory)_CD141, Dendritic Cell (Type 1, CD141+)_CCR5, B Cell (Plasmablast)_CD123, NK Cell (CD56+ CD16+)_CD80, CD8+ T Cell (Central Memory)_CD127, B Cell_unassigned_CD80, CD4+ T Cell (Treg)_CCR6, CD4+ T Cell (Naive)_CD14, CM- HLADR+_unassigned_CD27, Dendritic Cell (Type 2, CD1c+)_CD86, B Cell (Plasmablast)_CD80, CD4- CD8- T Cell_CD27, CM-_unassigned_CD57, NK Cell (CD56+ CD16+)_CD123, B Cell_unassigned_CD141, Plasmacytoid Dendritic Cell_CD56, CD4- CD8- T Cell_HLADR, CD8+ T Cell (Central Memory)_CD209, CM-_unassigned_CX3CR1, Dendritic Cell (Type 2, CD1c+)_PD1, CD4+ T Cell (Treg)_HLADR, B Cell (Plasmablast)_CCR6, CM-_unassigned_CD11b, Monocyte (CD14+ CD16+)_CD141, CD4+ T Cell (EMRA)_CX3CR1, CD8+ T Cell (Central Memory)_CD27, CD8+ T Cell (Effector Memory)_CD25, CD4+ T Cell (Treg)_CXCR3, CD4+ CD8+ T Cell_CD3, B Cell (CD27-)_CCR4, Dendritic Cell (Type 2, CD1c+)_CD161, CM-_unassigned_CD14, CD8+ T Cell (Naive)_CD27, Dendritic Cell (Type 1, CD141+)_CCR6, CD4+ T Cell (EMRA)_PD1, CM- HLADR+_unassigned_CD66b

Acute vs Conv

6.1.1 violin plot

Figure 7: Violin Plot DA lmm Acute vs Conv

6.1.2 mfi heatmap

Figure 8: Heatmap FDR < 0.05 DA lmm Acute vs Conv

7 Comparison of results per method

Acute vs Conv

7.0.1 Result by methods on Acute vs Conv

Union list cluster result

Acute vs Conv: Monocyte (CD14+ CD16-)_CD25, Monocyte (CD14+ CD16-)_CCR7, CD4+ T Cell (Effector Memory)_CD45, Monocyte (CD14+ CD16-)_CD209, Monocyte (CD14+ CD16-)_CHIKV, Monocyte (CD14+ CD16-)_CD11c, CD4+ T Cell (Central Memory)_CD45, B Cell (Plasmablast)_CD45, CD4+ T Cell (Treg)_CD45, Monocyte (CD14+ CD16-)_CD123, CD4+ T Cell (Effector Memory)_CD57, Monocyte (CD14- CD16+)_CD45, CD4+ T Cell (Naive)_CD45, Plasmacytoid Dendritic Cell_CD25, CD8+ T Cell (EMRA)_CD45, Monocyte (CD14- CD16+)_CD11c, CD4+ T Cell (Naive)_CD57, NK Cell (CD56+ CD16+)_CCR7, CD4+ T Cell (Central Memory)_CD57, Root_unassigned_CD45, CD8+ T Cell (Naive)_CD45, Monocyte (CD14+ CD16-)_CX3CR1, B Cell (CD27-)_CD3, CD4- CD8- T Cell_CXCR3, Monocyte (CD14+ CD16-)_CD16, Monocyte (CD14+ CD16-)_CD40, CD8+ T Cell (Central Memory)_CD45, Plasmacytoid Dendritic Cell_CD3, CD4+ CD8+ T Cell_CD45, B Cell (Memory)_CD45, B Cell_unassigned_CD45, CD4+ T Cell (Treg)_CD57, Plasmacytoid Dendritic Cell_CCR7, NK Cell (CD56+ CD16-)_CD45, Monocyte (CD14+ CD16-)_CD45, CD8+ T Cell (Effector Memory)_CD45, Monocyte (CD14+ CD16-)_CCR5, B Cell_unassigned_CD57, B Cell (Plasmablast)_CD57, CD8+ T Cell (Naive)_CD57, B Cell (CD27-)_CCR6, CD4- CD8- T Cell_CD45, B Cell (CD27-)_CD1c, Monocyte (CD14+ CD16-)_CD14, Monocyte (CD14- CD16+)_PD1, NK Cell (CD56+ CD16+)_CD3, B Cell (CD27-)_CD20, NK Cell (CD56+ CD16-)_CCR7, NK Cell (CD56+ CD16-)_CD3, CD4+ CD8+ T Cell_CD57, NK Cell (CD56+ CD16+)_CD45, CD8+ T Cell (Naive)_CXCR3, B Cell (Memory)_CD57, Plasmacytoid Dendritic Cell_CD45, CD8+ T Cell (Central Memory)_CD57, CD4+ T Cell (Effector Memory)_CD56, CD4+ T Cell (EMRA)_CD45, Monocyte (CD14+ CD16+)_CD40, CD8+ T Cell (Central Memory)_CXCR3, CM- HLADR+_unassigned_CD40, Monocyte (CD14+ CD16+)_CD123, Monocyte (CD14- CD16+)_CD40, B Cell (Plasmablast)_CXCR3, B Cell_unassigned_CCR7, CM- HLADR+_unassigned_CD123, NK Cell (CD56+ CD16-)_CD25, Monocyte (CD14+ CD16-)_CD57, Plasmacytoid Dendritic Cell_CD123, Monocyte (CD14+ CD16+)_CD11c, B Cell_unassigned_CD56, B Cell (CD27-)_CD45, CD8+ T Cell (EMRA)_CCR7, Monocyte (CD14+ CD16-)_CD141, Monocyte (CD14+ CD16+)_CD45, Plasmacytoid Dendritic Cell_CD161, B Cell (CD27-)_CD16, B Cell (CD27-)_CD57, Plasmacytoid Dendritic Cell_CD57, B Cell (CD27-)_CD127, B Cell (Plasmablast)_CD86, Monocyte (CD14+ CD16-)_CD3, Monocyte (CD14- CD16+)_CD141, Monocyte (CD14+ CD16-)_HLADR, B Cell (Memory)_CXCR3, NK Cell (CD56+ CD16-)_CXCR3, Basophil_CD45, Root_unassigned_CXCR3, CM- HLADR+_unassigned_CD14, Monocyte (CD14+ CD16+)_CD57, Monocyte (CD14- CD16+)_CD123, CD4+ T Cell (Treg)_PD1, Monocyte (CD14+ CD16+)_PD1, B Cell (CD27-)_CD25, B Cell (CD27-)_CD11b, Plasmacytoid Dendritic Cell_CCR5, Dendritic Cell (Type 2, CD1c+)_CD40, CD8+ T Cell (EMRA)_CXCR3, CD4+ T Cell (Effector Memory)_CXCR3, Plasmacytoid Dendritic Cell_CD141, CD4+ T Cell (Effector Memory)_CCR4, B Cell (CD27-)_HLADR, B Cell (Memory)_CD86, B Cell (Memory)_CCR6, B Cell_unassigned_CXCR3, B Cell (Plasmablast)_HLADR, B Cell_unassigned_CD11b, B Cell_unassigned_CCR6, Monocyte (CD14+ CD16+)_CCR7, CM- HLADR+_unassigned_CD86, Dendritic Cell (Type 1, CD141+)_CD123, Monocyte (CD14- CD16+)_CCR4, B Cell_unassigned_CD25, Monocyte (CD14- CD16+)_CD14, Plasmacytoid Dendritic Cell_CD40, B Cell_unassigned_CD1c, CD4+ T Cell (Effector Memory)_CD80, Monocyte (CD14+ CD16+)_CHIKV, Dendritic Cell (Type 1, CD141+)_CXCR3, Root_unassigned_CD1c, Dendritic Cell (Type 1, CD141+)_CD1c, CD8+ T Cell (EMRA)_CX3CR1, CD4+ T Cell (Naive)_CD56, B Cell_unassigned_HLADR, Monocyte (CD14+ CD16+)_CD14, NK Cell (CD56+ CD16-)_CD40, CD4+ T Cell (Treg)_CD27, CD4+ T Cell (Central Memory)_CD56, Monocyte (CD14+ CD16-)_CD20, CD4+ T Cell (Effector Memory)_CCR5, NK Cell (CD56+ CD16+)_CD25, B Cell (Plasmablast)_CD20, Dendritic Cell (Type 1, CD141+)_CD141, B Cell (CD27-)_CD56, B Cell (Plasmablast)_CD11b, B Cell (Memory)_CD20, CM- HLADR+_unassigned_CD57, CD8+ T Cell (EMRA)_CD11c, CD8+ T Cell (EMRA)_HLADR, B Cell_unassigned_CD20, CM- HLADR+_unassigned_CD45, B Cell (Memory)_CD1c, Dendritic Cell (Type 1, CD141+)_CD14, B Cell (Memory)_CD16, CD4+ T Cell (Central Memory)_PD1, CD4+ T Cell (EMRA)_CXCR3, B Cell (Plasmablast)_CD27, CD4+ CD8+ T Cell_CD56, Monocyte (CD14- CD16+)_CD20, B Cell_unassigned_CHIKV, Monocyte (CD14+ CD16+)_CD1c, B Cell (Memory)_CD127, Dendritic Cell (Type 1, CD141+)_CD80, Dendritic Cell (Type 1, CD141+)_CD45, CM- HLADR+_unassigned_CXCR3, Monocyte (CD14+ CD16-)_CD86, Root_unassigned_CCR5, CM- HLADR+_unassigned_CD20, CM-_unassigned_CD25, Basophil_CD25, Dendritic Cell (Type 2, CD1c+)_CX3CR1, CD8+ T Cell (Effector Memory)_CCR7, CD4+ CD8+ T Cell_PD1, B Cell (Memory)_CCR4, CD4+ T Cell (Effector Memory)_CD40, CD4+ T Cell (Central Memory)_CD27, NK Cell (CD56+ CD16+)_CX3CR1, NK Cell (CD56+ CD16-)_CCR4, CD8+ T Cell (Effector Memory)_CXCR3, Monocyte (CD14- CD16+)_CD3, Monocyte (CD14- CD16+)_CX3CR1, CD4+ T Cell (Central Memory)_CD127, CM- HLADR+_unassigned_CD25, Dendritic Cell (Type 2, CD1c+)_CD27, B Cell_unassigned_CD27, CM-_unassigned_CD11b, CM- HLADR+_unassigned_CD11b, Plasmacytoid Dendritic Cell_CD11b, CM- HLADR+_unassigned_CD3, Dendritic Cell (Type 1, CD141+)_CD86, CD4+ T Cell (Treg)_CCR4, CM-_unassigned_CD14, Dendritic Cell (Type 2, CD1c+)_CCR4, Plasmacytoid Dendritic Cell_CXCR3, CD4+ T Cell (Central Memory)_CXCR3, CD4- CD8- T Cell_CD57, NK Cell (CD56+ CD16+)_CD56, Monocyte (CD14+ CD16+)_CD3, Dendritic Cell (Type 1, CD141+)_CD20, CD4+ CD8+ T Cell_CCR7, CD4+ CD8+ T Cell_CD27, B Cell (Plasmablast)_CD123, Dendritic Cell (Type 1, CD141+)_CCR6, B Cell (Memory)_CD40, B Cell (Plasmablast)_CD40, CM-_unassigned_CD45, Dendritic Cell (Type 2, CD1c+)_CHIKV, Plasmacytoid Dendritic Cell_HLADR, Dendritic Cell (Type 2, CD1c+)_CCR7, CM-_unassigned_CD57, CD4+ CD8+ T Cell_CCR4, Dendritic Cell (Type 1, CD141+)_CD57, CD8+ T Cell (Central Memory)_CD127, B Cell (CD27-)_CCR4, CD4- CD8- T Cell_CD27, B Cell (Memory)_CD25, CM- HLADR+_unassigned_CD141, B Cell (Plasmablast)_CCR6, CD8+ T Cell (Central Memory)_CD27, CD8+ T Cell (Effector Memory)_CD25, CD4- CD8- T Cell_HLADR, CM- HLADR+_unassigned_CCR4, Dendritic Cell (Type 1, CD141+)_CD11b, Dendritic Cell (Type 1, CD141+)_CCR5

8 Union Graphics

8.1 Heatmaps on union results

Acute vs Conv

Figure 9: mfi’s Heatmap of consensus results for Acute vs Conv

Glossary

counts: Raw count abundances.
perCellCounts: Frequencies abundances.
perCellCountsNorm: Argsinh frequencies / 0.03 then centered by the mean per clusters.

R session info

R version 4.3.3 (2024-02-29)

R version 4.3.3 (2024-02-29)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C

attached base packages: grid, stats4, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: knitr(v.1.46), patchwork(v.1.2.0), htmlwidgets(v.1.6.4), diffcyt(v.1.22.1), checkmate(v.2.3.1), ggiraph(v.0.8.9), reactable(v.0.4.4), plotly(v.4.10.4), tibble(v.3.2.1), kableExtra(v.1.4.0), ggrepel(v.0.9.5), ggplot2(v.3.5.1), tidyr(v.1.3.1), data.table(v.1.15.4), colorRamp2(v.0.1.0), randomcoloR(v.1.1.0.1), RColorBrewer(v.1.1-3), ComplexHeatmap(v.2.18.0), SummarizedExperiment(v.1.32.0), Biobase(v.2.62.0), GenomicRanges(v.1.54.1), GenomeInfoDb(v.1.38.8), IRanges(v.2.36.0), S4Vectors(v.0.40.2), BiocGenerics(v.0.48.1), MatrixGenerics(v.1.14.0), matrixStats(v.1.3.0), dplyr(v.1.1.4), readr(v.2.1.5) and analycyte.utils(v.3.0.11.2)

loaded via a namespace (and not attached): splines(v.4.3.3), later(v.1.3.2), bitops(v.1.0-7), polyclip(v.1.10-6), XML(v.3.99-0.16.1), lifecycle(v.1.0.4), rstatix(v.0.7.2), edgeR(v.4.0.16), doParallel(v.1.0.17), lattice(v.0.22-5), MASS(v.7.3-60.0.1), flashClust(v.1.01-2), crosstalk(v.1.2.1), backports(v.1.4.1), magrittr(v.2.0.3), sass(v.0.4.9), limma(v.3.58.1), rmarkdown(v.2.26), jquerylib(v.0.1.4), yaml(v.2.3.8), httpuv(v.1.6.15), minqa(v.1.2.6), ConsensusClusterPlus(v.1.66.0), lubridate(v.1.9.3), multcomp(v.1.4-25), abind(v.1.4-5), zlibbioc(v.1.48.2), Rtsne(v.0.17), purrr(v.1.0.2), RCurl(v.1.98-1.14), TH.data(v.1.1-2), tweenr(v.2.0.3), sandwich(v.3.1-0), circlize(v.0.4.16), GenomeInfoDbData(v.1.2.11), svglite(v.2.1.3), codetools(v.0.2-19), DelayedArray(v.0.28.0), DT(v.0.33), xml2(v.1.3.6), ggforce(v.0.4.2), tidyselect(v.1.2.1), shape(v.1.4.6.1), farver(v.2.1.1), lme4(v.1.1-35.3), jsonlite(v.1.8.8), GetoptLong(v.1.0.5), survival(v.3.5-8), iterators(v.1.0.14), emmeans(v.1.10.1), systemfonts(v.1.0.6), foreach(v.1.5.2), tools(v.4.3.3), ggnewscale(v.0.4.10), Rcpp(v.1.0.12), glue(v.1.7.0), SparseArray(v.1.2.4), xfun(v.0.43), withr(v.3.0.0), fastmap(v.1.1.1), boot(v.1.3-29), fansi(v.1.0.6), digest(v.0.6.35), mime(v.0.12), timechange(v.0.3.0), R6(v.2.5.1), estimability(v.1.5), ggprism(v.1.0.5), colorspace(v.2.1-0), Cairo(v.1.6-2), utf8(v.1.2.4), generics(v.0.1.3), httr(v.1.4.7), S4Arrays(v.1.2.1), scatterplot3d(v.0.3-44), pkgconfig(v.2.0.3), gtable(v.0.3.4), RProtoBufLib(v.2.14.1), XVector(v.0.42.0), htmltools(v.0.5.8), carData(v.3.0-5), multcompView(v.0.1-10), clue(v.0.3-65), scales(v.1.3.0), leaps(v.3.1), png(v.0.1-8), colorRamps(v.2.3.4), rstudioapi(v.0.16.0), tzdb(v.0.4.0), reshape2(v.1.4.4), rjson(v.0.2.21), uuid(v.1.2-0), nlme(v.3.1-164), curl(v.5.2.1), nloptr(v.2.0.3), cachem(v.1.0.8), zoo(v.1.8-12), GlobalOptions(v.0.1.2), stringr(v.1.5.1), parallel(v.4.3.3), pillar(v.1.9.0), vctrs(v.0.6.5), promises(v.1.2.1), ggpubr(v.0.6.0), car(v.3.1-2), cytolib(v.2.14.1), xtable(v.1.8-4), cluster(v.2.1.6), evaluate(v.0.23), mvtnorm(v.1.2-4), cli(v.3.6.2), locfit(v.1.5-9.9), compiler(v.4.3.3), rlang(v.1.1.3), crayon(v.1.5.2), ggsignif(v.0.6.4), labeling(v.0.4.3), FlowSOM(v.2.10.0), flowCore(v.2.14.2), plyr(v.1.8.9), stringi(v.1.8.3), pander(v.0.6.5), viridisLite(v.0.4.2), munsell(v.0.5.0), lazyeval(v.0.2.2), V8(v.4.4.2), Matrix(v.1.6-5), hms(v.1.1.3), statmod(v.1.5.0), FactoMineR(v.2.11), shiny(v.1.8.1.1), highr(v.0.10), memoise(v.2.0.1), igraph(v.2.0.3), broom(v.1.0.5) and bslib(v.0.6.2)

References

Xie, Y. Dynamic documents with R and knitr. (Chapman; Hall/CRC, 2015).

Allaire, J. Quarto: R interface to ’quarto’ markdown publishing system. (2022).

Weber, L. M. Diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. (2023).

Reuse

Open Licence (Etalab)